On paint jobs that require the graphics to line up perfectly, I usually basecoat the parts on my stands, then wrap the bike in thin plastic, and put the parts back on the bike. Do the masking there, perhaps spray as well. Then off the bike and onto the stands again, to cut in edges, if necessary, and/or finish the clearcoating.
Nothing like doing it this way, mocking stuff up (off the bike) sometimes results in not-so-good surprises!
I painted an entire bike with the parts on it, with plastic under it, as the "basecoat" was HOK pearls, going from white up front, to dark red in the back, in a seamless transition, from white-yellow-orange-red. Then Candy purple graphics went over that. Since it was a show bike, it had to be perfect.