In general, the Perfect Layout plug-in aligns dynamic and expressive text expressions below the staff both horizontally and vertically.
Tempo and rehearsal marks, along with tempo alterations are aligned above the staff both horizontally and vertically.
All other expressions are left untouched.

Usually the plug-in first removes any manual adjustments, then looks for collisions and, should it detect any, moves the expression away from the colliding object.
If the horizontal offsets of the expressions are large, it is unlikely a clear zero position was intended by the engraver. In this case manual (horizontal) adjustments are not reset. The thresholds for these "extended offsets" can be set in "Reset Horizontal Position of Dynamics Until Maximum Horizontal Offset" and "dito., Max. Horizontal Reset Offset for Whole or Dotted Notes".

Dynamic expressions in staves with lyrics are very often placed above the staff.
Dynamic expressions placed above the staff are not taken into account by the plug-in and are not aligned.
The option "Reset Vertical Position of Dynamics and Expressive Text on Notes With Lyrics" is switched off by default. If selected, dynamics above the staff will suddenly appear below the staff line if they were taken from the default dynamics category and it is still set to below baseline.

Some expressions usually only appear in the parts, to not mess up the conductor's score. These expressions must be placed in a user-defined category containing the keywords defined in "Hide Expressions in Score with Category Keyword(s)".
E.g. if you name the expression category "In Parts Only" and enter the keywords "part,only", then the plug-in will hide all expressions from categories with names that includes these keywords.

Image 1: Category "In Parts Only"

Just as expressions articulations positions are usually first set to the vertical default position and then tested for collisions.
It is highly recommended to keep the option "Reset Vertical Position of Note Articulations, Fermatas, Bows and Ornaments" selected.
Only recognized articulations are reset, i.e. shape articulations or articulations with unknown music symbols are not reset, except for those shape articulations that are explicitly defined in the Perfect Layout settings (e.g. up/down bow shape articulation).
Articulations that are usually aligned manually (e.g. arpeggio) are not reset by default (see option "Also on 'Position: Manually' Articulations").

Certain articulations can be automatically hidden in the score. This might make sense for bow marks, breath mark commas or certain shape articulations (e.g. brass fingering).
These can be selected in "Hide These Articulations in Score Only".
By default, only bow marks are selected.
Note: Bow marks are only hidden on string instruments. So make sure to use a recognizable instrument name, a string instrument ID or a string sound.
The option "Reveal Accidentals on False Tied Notes" shows accidentals that were forgotten to add and only disappeared because of Finale's function to automatically hide accidentals if a note is tied.
This helps detecting wrong notes in playback or even wrong ties.
If the tie was correct, it also looked correct without the extra accidental. But if the accidental is revealed by the plugin, it will look wrong.
This option is more important if you work with playback. It is not recommended to use it, if you work without playback.

Image 2: Left: Original, Right: Hidden accidental revealed
It is recommended to let the plug-in remove all manual slur adjustments by selecting "Reset Manual Slur Adjustments". Otherwise slur optimizations may not work.
By default manual slur adjustments are removed, while manual curve adjustments are not because they are very often "hand-made" to illustrate a more complex behaviour.
To remove faulty manual note positions that were created accidentally, the Perfect Layout plugin has the option to do this automatically according to Finale's settings from Document Options. If the option "Automatic According to 'Manual Positioning' from Document Options" is selected, then it will either clear or keep manual adjustments of notes dependent on the 'Manual Positioning' setting from Finale's document options.

The option "Move Single Pitch Notes on One-Line Percussion Staves Onto Staff Line" is required for 1-line percussion staves where the notes are not centered on the staff line (see image 3). This occurs from time to time in older documents or when imported through MusicXML.
This feature only becomes active when only one pitch ("Single pitch") is used throughout the staff. It will not do anything for example to two-note conga or bongo staves.

Image 3: "Single Pitch Notes" on the percussion staff line (activated) and above the staff line (deactivated)

By default flipped stems in one-layer measures without slurs are corrected by Perfect Layout. With the option "Remove Flipped Stems Also on Slurred Notes" you can also activate this feature for notes under slurs.
The option "Reset Left Start Point Offset of Lines That Start on Beat 1" is helpful for most custom lines as it is difficult to place them with a horizontal offset 0 on first try.
But there are, of course, scenarios where this option should better be switched off (especially in contemporary notation).

Image 4: Left: Original, Right: Start position set to horizontal offset 0.
"Clear Manual Vertical Lyrics Positioning" removes all manual adjustments. They appear especially in imported MusicXML files.

Image 5: Left: Original, Right: After vertical reset

The option "Always Hide Empty Staves in Parts" was meant for multi-staff percussion instruments where the parts had to be optimized because of many empty staves.
The option "Keep All Instruments on First Staff System in Parts" makes sure that at least on the very first staff system all instruments are visible (for example, if it's a percussion part with multiple instruments).
If you want to exclude staves from hiding, make sure to deactivate "Allow Hiding When Empty" in Finale's Staff Attributes dialog.

Parts that only have a two staff isntrument (e.g. piano or harp) are currently excluded from this feature. If you want to optimize the staff systems of your piano part, you must do it manually.