[totaltec]

Phil is absolutely right. In addition to keeping your skin changes in a custom skin directory, you can build any php changes into a special module for your store. Just like existing XC modules, you can write your code to only run when your module is active, and put minimal edits in the core, just hooks that call your code.

This way your custom PHP changes are contained mostly in the module directory, skin changes in your custom skin. Avoid editing the existing tables in the database if you can, instead add new tables and prefix them with something that makes them stand out.