In my shared\ptxprint\projectname folder I have two style files, ptxprint.sty and ptxprint-mods.sty. I assume that ptxprint.sty is intended to be overwritten by Paratext (once PTXPrint is available from Paratext), and that styles that I want to create or update should go into the ptxprint-mods.sty file?
ptxprint.sty is overwritten by ptxprint and is the result of outputting the GUI representation of the stylesheet. It contains the differences from the stack of usfm_sb.sty then ptx2pdf.sty then your project custom.sty then your publication ptxprint-mods.sty. Thus if you have style changes you want to make textually rather than via the GUI then ptxprint-mods.sty is ideal. But I can see people using ptxprint.sty and the GUI more.
The Styles editor now has some help about this on the tooltip when you hover over the question at the bottom the screen:
