I started to use x-cart a little for some of my clients so everything I learn about the file structure, style design, programming etc I will continually add to this post.

Skin1/

Where all the design files are kept using - smarty template engine.

header.tpl The header info of the page

Skin1/customer/

Generally everything in the skin1>customer folder is to do with the front end of the store.

home.tpl is the home page

Skin1/main/

Skin1>main also has a few useful files

prnotice.tpl is generally where the copyright notice and footer contents goes.