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.