I think I've narrowed my problem further.

Currently my URL comes up as: www.mysite.com/store/?cat=1

I needthe URL to show up as any one of the following:
1) www.mysite.com/store/wordpress?cat=1 or
2) http://www.mysite.com/store/index.ph...ordpress&cat=1 or
3) http://www.mysite.com/store/?index.p...ordpress&cat=1

Basically I need to add:
1) "wordpress" before of "?" or
2) "index.php?main_page=wordpress&" after "?"