Why do you want to sell licenses?
As mentioned earlier, you can go at least three ways:
1. Trust your users and do not encode any file and sell the skin at a low price, so that it would be easier/safer to buy the skin from the trusted place/market/site.
2. Do not encode any file of a skin either, and write a script to autoupdate the skin, and on the server side you would check whether or not user has a valid license to download a skin. Darwin Skin seems to follow this way. Quick way to run skin.
3. Add in skin files PHP code which would include an encoded PHP script which would periodically connect to your server and verify license. License verification will slow down browsing DA in certain cases. And what if your server will be down? How much will an user allowed to use the skin without verification? And what your PHP code will do? It should add extra functionality...What if they remove the PHP script or replace it with an empty PHP file? If the only purpose of a PHP script to verify license your skin will be easily nulled. CyberAdmin skin seems to follow this way, they add extra functionality with custom PHP script and verify licenses with it.