Your clone stays as it was when you made it. When the original skin is updated, you choose which of its changes you want in your clone. The Compare tool shows them.
On the Templates tab of your clone, the Compare button shows which templates differ from the original:
If the original skin has templates your clone doesn't, they're listed under New Templates Not In This Skin. Import copies one into your clone.
Click Compare. Your template is on the left and the original on the right, with the differences highlighted.
The original's skin name is replaced with your clone's name in the comparison, so that only real differences are highlighted.
Compare works on any template, not just in clones: it shows your saved changes next to the template file.