Enter all notation symbols as Finale® places them by default.
Don't waste time in manually correcting the placement of hairpins, custom lines, expressions or articulations.
That's what the plug-in is for.
But make sure that the symbols were not placed
ambiguously.
Otherwise the Perfect Layout plug-in might not optimize the symbol's layout as it is not clear which beat or which symbol it was originally intended to connect to.
Example 1:

Image 1:
Left: Unclear on which beat the hairpin should end
Right: It should end at the end of the measure
Example 2:

Image 2: Finale's placement options are very flexible, but sometimes it is difficult to detect if a placement was intended or is faulty.
Left: Overlapping connection points. Was the hairpin intended to be in the first measure or in the second measure on beat 1? Why is mf connected to beat 3?
Right: Clear placement
Rule 1:
The plug-in will only change the placement of symbols, if it is very likely that the new position was originally intended.
(In other words: If in doubt, leave it out.)
The good news is:
The plug-in already has many rules for detecting and automatically fixing these scenarios.
For example a little offset or a little overlap usually is no problem, as in these examples:

Image 3: Overlapping hairpins that are connected to the same measure position are automatically corrected by the plug-in and horizontally optimized (at the start, the middle and the end).

Image 4: Overlapping unambiguous expressions are automatically corrected.

Image 5: Overlapping expressions and hairpins are automatically corrected.
Rule 2:
The clearer you place symbols, the better they are automatically optimized by the plug-in.
Don't be overprecise, that's the job of the plug-in.
Recommendations for optimizing your Finale® default document:
1.)
Smart Shapes: Turn on "SmartShape->Snap When Attaching to Beats"
2.)
Expressions: For a more uniform look it is recommended to have all expressions in an expression category use the "Category Positioning" instead of individual positioning settings.
This is especially recommended for dynamic expressions, tempo marks and tempo alterations as these symbols are usually on the below or above baselines and vertically aligned.
3.)
Articulations: Optimize the default placement of articulations as this is where the plug-in usually moves the articulations - except when there are collisions.
E.g. if you want to have an articulation appear
below the note, don't use the placement "Position: Above Note" and move it manually below, but use "Position: Place Below".
If necessary, you need to create duplicate articulations with different placement settings.
Things to avoid:
- Having two dynamics at the same measure position (except f p which becomes fp).
- Having dynamics
between hairpin start and end points (unless this is what you want).
- Having dynamics and hairpins overlap and/or connect internally different than visually (as in image 2 above).