Hi Kyle,
The .skys files are a way to save Skyline settings so that they can be stored, shared, and loaded back into Skyline through the Settings > Import menu item. The settings saved by Skyline to a .skys file must first be saved through Settings > Save Current, which causes them to appear as a one-click menu item in the Settings menu for changing to the saved settings. When you use Settings > Import to load a .skys file, it also adds these one-click menu options to the Settings menu, allowing you to quickly switch to these settings at any time in the future.

All that said, we tend now to favor template Skyline documents, which may contain no targets, but once loaded contain all of their saved settings.

But we leave it up to you to choose between 2 options of sharing settings. You could create a .skys file with all of the baseline settings options you want to share, say with your labmates, or you could create a set of blank Skyline template documents, i.e. a collection of .sky files.

Hope this helps to clarify the intention of the .skys files and saved settings on the Settings menu. Thanks for using the Skyline support board.

--Brendan