Allot of it would depend on the piece that you are powder coating, I have done allot of yeti tumblers and for 2 colors I would put a base coat on the whole cup and cook about 50 to 75 percent of the cook time then put the vinyl stencil on and spray the second color and cook for about a minute then remove and peel the vinyl off and cook it for the whole time. I have never seen a difference in over cooked powder, I’m sure that I have had some in there longer than what it was meant for.
Mancrafting on youtube has allot of videos on powder coating and watching him is what got me into powdercoating. I’v seen him on here a few times, check out his channel if you are thinking about powder coating.
For larger items like this Halloween sign that I did for my wife I sprayed the orange and white then used a shop vac with a small brush to clean up the overspray and get close to where I wanted the colors to change. I then cooked it for about 7 minutes on a 12 minute powder, took it out and let it cool then taped off the orange and white and sprayed the texture black on the rest of it and put it in the oven for about 1 minute then pulled it out and took off the tape and cleaned off the glue residue from the tape then cooked it for the 15 minutes that the black required.
Good luck, it’s allot of fun, and frustration at times, lol