I am thinking about getting a GP cub with the cloth covering and would like to do something different with the color scheme. Can you just paint over the covering with something like monokote spray paint?

Whether you can use Monokote paint or not should be checked carefully. It's fuel proof up to 15% nitro but it has a tendencey to eat its way through some other paints. Try to get some of the covering material as used on the Cub. Use a small bit for a patch test. Tower should be happy to help if you intend to buy the airplane from them.