Is it red or green to switch for it to be in phase with the middle pickup? Another question is, is there any reason I would not want it to be in phase?
That would depend on what middle pickup you have. Its easy to swap, so I'd wire the red as hot and green to ground. When you test it, with the bridge + middle, if they're out of phase it will sound very thin and weak.

Out of phase can give some useful sounds (mostly used by blues guys or for clean tones) but most of the time you'll want them in phase.