There are many scenarios where multiple expressions on the same measure position or colliding horizontally can occur. Perfect Layout can handle many, but not all of these cases yet.
The following two images show a before/after Perfect Layout look demonstrating some multi-expression cases (created with v2.023).
It's also available as a real-time video and as a Finale document for download.

Image 1: Handling Multiple Expressions (before Perfect Layout)

Image 2: Handling Multiple Expressions (after Perfect Layout)

To prevent expression collisions please note:
1.) If possible, don't stack more than two Rehearsal/Tempo expressions (see m.10 in image 2).
Workaround: Create a mulit-line expression instead of several single line expressions (as in m.4).

2.) Be careful when you use several Technique Text expressions on the same side of the staff (see m.1 beat 4 and m.2 beat 1).
If the expressions don't overlap, the top expression is kept at that position (m.1 beat 4, supported in PL v3.0177+).
Otherwise the expression with the smaller expression ID is put on top (m.2 beat 1, supported in PL v3.0177+).
Or, you could put one expression below and one above the staff (m.2 beat 2) or attach them to different measure positions.

3.) If you put Technique Text expressions after or onto a dynamic expression, make sure it is still clear to the reader on which beat the technique is to be applied (see con sord. m.10-15).
If placed after the dynamic on short notes (m.15), it may be unclear. In this case it might look better, if placed above the staff.
You could also add ALLOWSHIFTRIGHT to the expression's description text: in that case the text expression would automatically be shifted to the right of the dynamic (see description here).

4.) As an exception of 3.) PL moves text expressions with an italic font style behind dynamics as it assumes that these are actually Expressive Text expressions which are clear enough to the read, even if placed after the dynamics.

5.) If 1.), 2.), 3.) and 4.) is not possible, then place your expression manually before running the plug-in and add EXCLUDE to its description text in the Expression Designer dialog.
Perfect Layout will then omit the expression. Beware that this also may affect other occurences of the expression in the score.
In this case: duplicate the expression and create one expression with and one without the EXCLUDE mark.
More about the EXCLUDE and INCLUDE tag can be found in the "How to use"-document.

6.) If a Rehearsal/Tempo Mark mark on beat 1 collides with a rehearsal letter in the next measure, Perfect Layout can broaden the measure and even move other measures to the next system (see m.3 for broadening and m.6 for moving to the next system).
Make sure to have "Preferences->Edit->Reflow Measures->Across Systems" and maybe even "Across Pages" activated, otherwise this feature might not work properly if there is not sufficient free space for broadening the measure.

7.) Tempo Alteration expressions attached after beat 1 may collide with rehearsal letters/mark in the next measure (see m.8/9).
Perfect Layout doesn't remove this collision by default (by shifting the the rehearsal letter up), because a manual/individual solution looks better in most of these cases.
Nevertheless this feature (Shift Rehearsal Letters Up on Tempo Expression Collisions) can be activated on the "Alignment"-tab (as of PL v2.023).

8.) Two dynamic expressions "f" and "p" on the same measure position are horizontally aligned to "fp" (m.8).
If you require the rarely used "pf", please create it as a single expression.

9.) Dynamics together with "expressive text"-custom smart lines (e.g. "f" + "cresc. - - - - - - -") are currently not aligned automatically by Perfect Layout yet.
Workaround: Use expressive text expressions ("cresc.") instead.
This is on our to do-list for on one of the upcoming updates.

10.) When running Perfect Layout on an old or MusicXML-imported Finale documents, make sure to apply it at least the first time to the full document.
Perfect Layout optimizes many expression default positions, especially in old/MusicXML documents.
But this function is only activated when running the plug-in on the full document as otherwise inconsistencies may occur.
"Old" means in this case created before Finale 2014.

To get the best results with the Perfect Layout plug-in it's important to use Finale®'s expression categories correctly.
The same goes for Finale®'s other default categories:
1.) Dynamics/Niente Circle: Keep dynamics only in a category with the keyword "Dynamics" (or Dynamik or dynamiques or dinamiche from the international editions of Finale). It's also possible to combine words like "Percussion dynamics" or "Above Staff Dynamics" - as long as the main keyword is found.
2.) Expressive Text: Expressive text expressions are partially taken into account in alignment. Especially in combination with dynamics or hairpins on the same measure position the expression will be aligned horizontally and/or vertically.
3.) Rehearsal Marks/Tempo Marks/Tempo Alterations: Elements in these categories are taken into account for vertical and horizontal alignment above the staff. Rehearsal Marks can also be placed at different positions at the beginning of a staff (see alignment tab).
4.) Technique Text: Expressions in this category are not vertically/horizontally aligned!
5.) "Cue"-Keyword (user-defined): see Layer/Cues tab.
6.) "In Parts Only"-Keyword (user-defined): see Reset/Hide tab.

If you use expressions with numbers only, the plug-in can move them into the Rehearsal Marks category, if these options are checked. Numbers with rectangular expressions can be automatically moved (Option "Move Number Expressions with Non-Circular Enclosure to Rehearsal Mark Category"). Numbers with circular enclosures are typically fingerings and will not be moved automatically.
Measure number expressions can also be moved automatically: the plug-in compares the expression number with the measure that the expression is used in and if it fits, it will be moved (Option "Move Measure Number Expressions to Rehearsal Marks Category").

Note 1:
For best alignment use as few expressions in one measure position as possible.
E.g. "più f" or "pp sub." should be a single expression. The horizontal alignment (not centered as in standard dynamics, but left- or right-aligned) is automatically applied in these cases.
The same goes for tempo marks and rehearsal texts:
If you have for example the four above staff lines "M" (=Letter M), "Andante", "q=100" and "Verse" don't use four expressions on top of each other, but only two: use the rehearsal mark M plus a single expression for the text.
The Perfect Layout plug-in has a few cases where multiple expressions are aligned correctly, but it becomes difficult if it is more than two of the same type.

Note 2:
If you have imported a document through MusicXML, it performs an automatic category assignment if the whole score is processed with the Perfect Layout plug-in: If the plug-in detects typical keywords, it suggests to move the expressions to the corresponding category.
This works very good with dynamic expressions and also with a few standard expressions from the other categories. But especially if you use less common or foreign texts, the automatic category detection does not work. In this case it is important that you move the expressions to the correct category before applying the plug-in. Otherwise not all features will work.

Compound dynamics like poco pp, sub ff. or molto f require extra attention because they are often so wide that their placement may be ambiguous (image 3).

Image 3: Ambiguous dynamics - does it start on beat 1 or beat 2?

Note: For subito expressions it is recommended to always use "f sub." instead of "sub. f" or "subito f" which usually makes it more clear in the score by default.
More examples of non-recommended subito use are in m.3 in image 5 further down.

Image 4: sub. f and subito f are difficult to read; f sub. is clear

Perfect Layout offers three options for horizontal placement of these compound dynamics (for examples see image 5 below).
In PL Gold you find this option on the Expressions tab, in PL Silver on the Alignment tab.

1.) Align to the Center of the Dynamics Symbol (default option)
Based on the suggestions by Gould in Behind Bars this algorithm always centers the expression under the dynamics symbol if the expression starts with a text (like poco, molto, sub.). On barline collisions an opaque background is automatically added.

Note: Make sure to have any expression in the expression dialog that already uses any enclosure.
In Finale enclosures/opaque backgrounds can only be copied and modified from existing expressions, but not created automatically if no expression uses an enclosure. There will be a warning message if Perfect Layout hasn't found any expression with an enclosure.

2.) Align to the Center of the Full Expression and Don't Break Barlines
This option prefers align to the center of the full expression and prevents barline collisions by shfiting the expression away from the barline.
Although this style has been frequently used in previous centuries and handwritten scores it often leads to ambiguous placement of dynamics (see m.2 below in image 5). Please use this option with care or switch to option 3 ("Flexible") which prevents ambiguous placement in most cases.

3.) Align: Flexible
This option is a combination of 1. and 2. It allows crossing barlines by adding opaque backgrounds to prevent ambiguous placement.
If the bar is not ambiguous (e.g. a wide dynamics under a whole note, m.6 in image 5), then it will be shifted away from the barline.
If there is enough space, it will align to the center of the dynamics symbol (e.g. m.4 in image 5).
Otherwise it will align to the center of the full expression.


Image 5: Overview of the options for compound dynamics placement

You can remove the opaque background from rehearsal and tempo marks/alterations with the option "Remove 'Opaque' from Reh./Tempo Marks".
Note: in PL v3 only expressions with no border are taken into account. Opaque background on expressions with a line width above 0 are kept as they are.
Usually the opaque feature is not required for rehearsal marks after applying PL, as the plug-in will remove all collisions anyway. Nevertheless it's possible to fine-tune this feature by the selection list which includes
"Don't Remove",
"Remove If Most Expressions Are Opaque" and
"Always Remove".

If the lowest element on a measure or staff is above the lowest baseline, the dynamic expressions can be shifted upwards (Option: "Shift Dyn. Epxressions Up by XXX If Lowest Element is Staff Line"). By default Perfect Layout will search the whole system for the lowest element. If "For Lowest Element Only Look at Expression's Measure" is selected, it will only analyze the measure of the expression for the lowest element.

Also check "Alignment->Align Dynamic Expressions Only If Connected by Hairpins". If this is not activated (which is by default in parts), it may lead to dynamics being vertically aligned which override the "Shift up" value.


Image 6:
Left Measure: Default placement of dynamics at baseline
Right Measure: "Shift up by 6 EVPU" and "For Lowest Element Only Look at Expression's Measure" activated

You can set the vertical distance of dynamic expressions to many other notation elements.
To optimize the look some dynamic symbols (mf, sf, rf, f) can get reduced offsets which better fits their skyline.

You can set the vertical distance of expressive text expressions to slurs and ties.