Generally they use masking for two-tone designs, then pull it before it goes in the oven.
For the BB shell, head tube and seat tube mfg's actually just use a laminated cardboard--the same that's used for packaging bikes. Any bike shop will have this laying around. For bottle bosses/fender eyelets, just use a bolt threaded in partially. You can use a wooded chopstick for the seat stay brake bridge.
One tip though: if you're not re-using the headset and BB, just leave them in. This will prevent you from having the face them after painting. Just score them with a utility knife before removing them. When I worked at a mfg that did paint in house and we had our own frames re-sprayed, that's what we'd do.
I do kinda miss having ready access to a powder coating facility! Cost for a frame painting was generally lunch or a six pack, and turn around time was half a day.
