The emptriv questions are stored in a "questions" subdirectory. It does run with cwd=<path to emptriv> but that's probably just my sloppy coding.

It is probably easiest to just install all packages on the software partition(s).

Right, which is why I was hoping that hda5 could be used for the "standard" stuff (the /empeg stuff plus /bin, /usr/bin, etc) and hda2 could hold all the user apps. But I guess you're right in that it doesn't make much sense to have it only available for Linux, which, without e2fstools on Win32, would be the case. I still think it's the ideal solution though.