Tough learning curve on this stuff indeed
The templates are made up of a combination of HTML, CSS and Smarty. Smarty is the toughest part to get the hang of, but the nested table layouts are also tough.
Honestly the best way to learn it is to just dive in and start getting familar with what is what. Webmaster Mode will help you with which templates control what. Once you know what to edit, you can either edit the code directly, or you can also get a plug-in for Dreamweaver that will help you view/edit the templates:
http://forum.x-cart.com/viewtopic.php?p=79807
You probably won't touch the php portion of the files that much, but some mods will require that as well. You need to access those files via ftp, as you can't get to them from the admin area of X-Cart.
Your best resource is this forum. Most of the common questions (which template is this, how do I make my cart do this, etc) have been answered hundreds of times, so be sure to search thoroughly. Hint: use 'and' in your searches - instead of searching for 'welcome text' search for 'welcome and text'. Improves the search results a ton.
If all else fails, post a question and we'll hook you up with the solution
Good luck!