Anevaude, I am assuming you know about the setting where one can designate the path for the store's main page. I did try to do a workaround where I created a different page than "Store" and then put the Cart, Account pages under that, and things almost worked with Permalinks enabled, but the Cart66 developers told me that changing that page does screw up the plugin's code and ultimately won't work.
After going back and forth with Cart66 (very helpful) and the hosting company, Hostway (NOT helpful: said looking at .htaccess issues was beyond their "scope"), my client decided to follow the advice of Cart66 and switch the site's hosting company to HostGator. I can,so far, highly recommend using HostGator for any site using this plugin. Their business plan was about $10 more than Hostway's per year, BUT, the business plan includes a free SSL certificate you can set up in the account add-ons section. Authorize.net (which is the reason I got this plugin in the first place) requires SSL certification from a site's owner in order to set up an account. File this under "Things I wish I knew before installing this Plugin".