If you have the version where the xcart skin is a module, you need to install the latest version. The skin named default is xcn in this version. http://next.x-cart.com/download/trial
Priority is always with the default skin and the template engine overrides the default skin with yours. This way you only have to replace the parts you require.
It would be useful to look at the xcn skin to get an idea of how it all works. There two places where replacement skins are placed currently. (odd to me)
skins/default/modules/<Your DevId>/<Your Module>
this is for your modules obviously. Notice that XLite\Module\ where you place your module does not have an 's' on the end but the default/modules does. Just pointing it out as when you type a namespace in it's easy to make a mistake and wonder for hour or so as to whats wrong
skins/<your skin name>
If you go litecommerce.com
and follow the link through to the wiki you will find some useful if not confusing information.
Skinning the Drupal version is much easier believe it or not.