I think your best bet is to check a theme that has the setting you're looking for or look through the personal files to see where similar things might be. (look under right click -> litestep -> edit config)

If that doesn't help, maybe you could give some specific examples?

Technically, all of those other .rc files are included into step.rc, so putting something in theme.rc or personal.rc will effectively put it into step.rc. When a module says "put this in step.rc" what it means is to put it in a file that is ultimately loaded by litestep as if it were in step.rc. If you put it into an .rc file that wasn't included, it wouldn't really do any good.