I went through this last year. I completely dismantled the frame and had it all powder coated except my lopros because I think it looks more professional that way, plus the new lowpros look cool. The frame is still full break-downable. I didn't do any masking because I didn't need to but the powder coater told me he could have.
Keep in mind for all of you Powder coated frame owners. powdercoating may be the most durable paint but it still wears off and leaves exposed aluminum to stain your tubes. Even if you have a frame that is built buy the most super duper, advanced, double secret frame builder in the universe. (That will be another story for later) but the point is that I still protect the bottom of my frame with gorilla tape. see this thread. Preventing Al transfer (drybox, frame, etc)