If you have water in your basement you should get it fixed before you paint. Water can cause damage to your foundation and can actually cause your basement to mold. Waterproof paint would be a good choice for a basement though.
water proof paint is not a bad idea. but before you apply water proof paint, a primer/sealer suck as KILZ will kill and mold that may currently be there as well as prevent mold from growing.
No it isn't a good idea to be using waterproof paint in a wet basement. The main reason is that you need to prep the area like all area's. Before painting wash and dry completely then apply according to the waterproofing instructions.
Many waterproofing paints can be used in damp conditions and even on active water leaks. If you have issues with water in your basement,waterproofing paint is the best paint you can use.