Layers and Cues

If your document uses linked parts with "Specify Vocing" and "Selected Notes Only", please activate the option in the Perfect Layout dialog.
Unfortunately JW Lua can't read these settings automatically. In these cases Perfect Layout runs slightly slower as it is more difficult to detect which notes appear in which part.
The plug-in can move all notes that were accidentally inserted in upper layers to layer 1. It doesn't do it when the layer has different playback attributes or if it contains resized notes (probably cue notes).
The option "Remove Unnecessary Use of Layers 2-4" is checked by default.
The following before/after images give an overview of Perfect Layout's cue text and cue note features (Image 1: score look, images 2-5: part look).
The Finale documents of these cue examples can be downloaded from the example page (Example 5).

Image 1: Cue texts and cue notes in the score before/after applying Perfect Layout.

Image 2: Timpani part: A two-layer cue with non-fixed lyrics size text font on layer 4 and melody cue on layer 3.

Image 3: Glockenspiel part: a single layer cue with fixed lyrics font size on layer 3.

Image 4: Perucssion part: a single layer cue with melody only, hairpin will be hidden for simplification.

Image 5: Drum Set part: cue text only which automatically breaks the multi-measure rest in the part as it was part of the "cue" expression category.

All cue options in detail

The Perfect Layout plug-in has a few functions dedicated to cue notes and cue texts. During initalization of the plug-in it tries automatically detect the "Cue Note Layer" and, if used, a "Cue Lyrics Layer w/Hidden Notes" (which some use for lyrics scaling).
If no cue notes were found, then these options ("Dedicated Cue Note/Lyrics Layer") cannot be set.
The plug-in processes cue texts created with Finale's "Add Cue Notes" plug-in like "Fl." or "Trb.1" if they are placed in a dedicated expression category. To detect this expression category it looks if the category names include the keyword listed in the option "Keyword for Categories with Cue Expressions" (set to "cue" by default).

Image 6: Cue expressions category
If the option "Scale Cue Expression with Note Entry" is selected, then the cue expression will get be reduced like the note entry (activated by default).
It's possible to let Perfect Layout hide some symbols in cue measures: hairpins and custom lines are hidden by default (Option: "Hide Hairpins and Custom Lines In Cue Measures"). In the Gold edition you can also automatically hide trills (Option: "Hide Trills in Cue Note Measures", deactivated by default).