I mask them and then paint them if there aren't stripe decals provided in the kit. Sometimes I paint them anyway depending on the quality of the decals.
If paint is bleeding under your masking tape something is wrong. It either isn't sticking properly, you aren't burnishing the edges down well enough, or you are putting a ton of paint over it. Paint the edges with Future before painting the color stripe. That way if anything bleeds it is just clear Future.