In XCN there are many improvements which allow you to modify the design without duplicating-modifying-replacing template files:
1. First of all, you can add your html snippets into existing templates by adding @ListChild directive. This is what Cpt.Crashtastic
named "russian dolls": http://forum.x-cart.com/showpost.php?p=345355&postcount=5
2. Most of the design tweaks can be done from CSS without hacking into the html templates.
3. The template engine prohibits the use of a complex logic in template files. All complex presentation logic is isolated in widget classes which you can extend/"decorate" from custom modules without copying the files (and duplicating the bugs, if any).
You may replace a couple of templates in your skin module - just be more careful when installing upgrades. If something goes wrong you always can temporarily disable the skin module and check how a new feature/change looks like in the "default" version (and then adapt your modified templates to reflect the change).
But you should never edit core files (including templates) - the next upgrade will drop them and replace with unmodified versions from the new version.