Phat Cats are really bad wired in series. 4-way wiring with series is useful with Telecasters, because those pickups have such clear string definition they can be wired series without getting muddy. SD Phat Cats are not that tonally different from PAF humbuckers, and wiring them series just results in a very, very bass-heavy tone.
Treat the Phat Cats like you'd treat humbuckers. That's the best way to think of them.
Obviously, since they're actually single coil pickups, they can't be split, as you asked about earlier.
Phase reverseal can be interesting with Phat Cats, but that is only an option if you pay extra to have the SD Custom Shop make them with the additional wire necessary.
As far as pots and capacitors go, it depends on the guitar. Phat Cats were designed with one 300k pot and one 500k pot, but SD use a fairly balanced/slightly bright guitar to do most of their designs, and in warmer guitars most people use two 500k pots instead.
The capacitor is entirely personal preference. There's no right or wrong value to use. Just decide how much treble you want the tone controls to roll off and pick the value that matches that. Bear in mind that Phat Cats are much warmer than other P-90 pickups, so you may want to use a weaker tone control than you first think. Again, treating them like you'd treat a classic humbucker is the best way to think through these things.