I usually adjust the bridge pickup as close to the strings as I can without the strings hitting the cover and making weird clicky noises. It is, after all, a low output A2 pickup, so no worries with string pull, really. I pick hard, so that's usually around 2.25-2.75 mm for the lowest string. That's usually the fattest and hottest you can get a pickup to sound.
I adjust the neck pickup to match the bridge pickup in volume. With Phat Cats, since the DCR and output is so close, I'd have it lower.
That's usually a rule of thumb for all pickups for me. The closest I can get them without it causing issues, the better. Of course, high output ceramic monsters tend to live lower because they pull on the strings harder, and with them too close, chords sound kinda pitch-y, I find.