First of all, I think you need to put your site under CVS if you haven't already.
Then, I recommend changing index.* to match your needs, rather than moving the file. You do need an index file. If you want, you can copy the index files to some other file name, but you should probably start working off of the index files, instead of moving them somewhere else.
There is a gap in the documentation here. But the index page does give you some ideas of where to go from startup. You can look at this page:
http://rubick.com/openacs/getting_started/
I'll need to get that page looking better, but it's somewhere to start.
