What you do is add them as Baggage Files. (File > New > Baggage File)
Thanks, I think I checked this out a while back but didn't use it because you can't put in altered files but it does work for added files. So that solves some of my problems.
But if you want to customize whstart.js, for example, you can't put that in there because it will be overwritten by the generated version.
One problem with generated files can be corrected by modifying this file (replace "vertial" with "vertical"):
C:\Program Files\Adobe\Adobe RoboHelp n\RoboHTML\WebHelp5Ext\template_generichtml\whgdata\whnvp30.htm