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.