Where to start?
 

I'm trying to completely change the structure of my store, since it needs to match my site. I'm very proficient in PHP, but the file structure is confusing me. What are the main files I need to edit? I can't even figure out which file is the main page file, onto which the various templates are loaded.

Your best bet is to use Webmaster Mode to see which templates are which. Unfortunately, PHP isn't going to help you with the tempaltes, as they are html/css/Smarty. The main customer side template is customer/home.tpl...that is a good place to start :)

Great, figured it all out, thanks! I ended up getting rid of a lot of the templating stuff since we only wanted the shopping cart, not the whole site.

Thanks again!