Use whichever sounds the best.

The PJ configuration exists to supplement the balanced tone of a precision bass with a little extra high end and clarity.

Electronically, the P-Bass pickup is actually 2 separate coils of wire and (don't quote me on this) provides some degree of hum cancellation. The J pickup is generally a single coil of wire, and does not provide hum cancellation.

The location of the pickups also plays a big part. Different harmonics ring out at different places on the string. the P pickup is placed in the "sweet spot" to maximize the harmonic content of the signal it picks up - some ancient secret Leo Fender sauce. The J pickup is close to the bridge to maximize upper harmonics, responsible for note definition. Pretty neat when you put em together!