Not to throw out a cliche, but the sky is the limit. I guess how I would do it depends on me, so how do you like to mess around? If tone is kind of important you could use a stack pot, like a 62 RI Jazz, for one control. It could hold the master tone for all three pups. I would incorporate push-pull pots for any tone mod that I would not use all the time - so for your humbucker (is it a mudbucker or something else like a DiMarzio?) you could have the push/pull mod the wiring from series to parrallel, and you can do that to the P pup as well. I don't know how hard it is to get those S-1 switches from Fender, but that is a neat trick to do the same thing. You could have a push/pull pot to bypass the tone as well. I personally don't like mini toggles, so if I can replace one volume or tone pot with a push pull I do that. In theory you could have all three pups run in series, or anything else you can think of. I try to limit myself to Sleeper mods, to use a hot rod term.
My personal concept is if you don't like a pup, you can turn it down, so I would use push pulls to alter wiring.
I almost installed a mudbucker in an old Fender, and didn't have the heart to cob it up. There was a thread here about other people who have done it besides Billy Sheehan, and it was not unknown in the 60s. I would do it to an aftermarket body or copy.
