Incorporating a store into Atahualpa

Our itsy bitsy record label has purchased software to create a download store for music.

I still have to style the CSS of the store to match our site (which is still in the testing phase), but I am curious if there is a safe way to incorporate it into a series of wordpress pages, or at least, modify the permalinks so people can just type in our domainname.com/store, or domainname.com/store/artist and be directed there. Right now, this is the rather unwieldy url.

http://midriffrecords.com/process.ph...tProcess-Start

I have a permalink plugin for WP 2.7.1 that so far has been great for all my pages, and I am wondering if I can utilize that somehow?

Currently, my Atahualpa site is in the testing phase at midriffrecords.com/midriff_TEST, so the store and test site are in different directories. But once I go live, they will all be in the same directory.

If resolving this issue requires a different order of donation or compensation, PM me privately, I would be happy to discuss it, Flynn. Thanks in advance.

Tony