Agreed, just make a copy of a cPanel theme and proceed with modifying it to your needs. I recommend editing the copy as if you edit the actual theme directly, your customizations may be overwritten by a future cPanel update if there are improvements made to the base skin.
I recommend using X3 as a base because it is cPanel 11 aware. Note that our theme editor for X3 is fairly flexible as-is especially when you start performing CSS customizations. Depending on what you are trying to do, you may not need to customize the code of an entire theme.