Need help – ecommerce site within wordpress site

Hi, I need help on this one. I have a wordpress site http://www.mysite.com and an OpenCart installation in a sub-folder called store (www.mysite.com/store)

Right now I have an under construction plugin working but already I can see that wordpress is going to interfere with the OpenCart installation. I gather that I need to modify the wordpress htaccess file in root (and perhaps the opencart htaccess file in store root) but don’t know what to do. I’m getting 404 errors when I click on my products etc. Can someone point me in the direction of what to do?