This zipfile includes a sample "wiki2.pl" file. This is intended as an example of how to cheaply run multiple wikis on the same site, without duplicating too much code. You only need one copy of the main wiki.pl file; the others should be copies of wiki2.pl, suitably adjusted. (wiki2.pl is only a few lines long.) In general, the alternate wikis will point to different data directories. This makes it easy to keep multiple, completely isolated wikis.
Caveat Emptor: I haven't even tried this download myself, so I'm not entirely certain it currently works. And this is, I reiterate, alpha-grade code -- undoubtedly buggy in a variety of ways. But if you want to play with ProWiki and kick the tires a bit, feel free.