This is really a matter of preference with no particular right answer and only one wrong answer: if the pickups are too close to your strings you will experience a phenomenon known as 'magnetic string pull' (guitarists call it strat-itis) which sounds like a wobbling, pulsing effect when you play in the higher frets.
Here's how I set pickup height:
- solo the bridge pickup
- raise the bridge pickup to a nominal starting point (for passive pickups I start with 1/8" from the string measured when pressing down the string at the last fret. For active pickups, I go even closer. Your bass has strong humbucking pickups so you may need to start a little lower)
- plug into your amp at a reasonable volume (not whisper quiet) and play the E & A strings from the 15th to the last fret and listen for the wobbling string pull sound. If you hear wobbling, lower the pickup in very small increments (a ruler that measures in 1/32 or 1/64" is very useful for this). If you don't hear wobble, raise the pickup in very small increments until you do hear it, then lower it just to the point where the wobble goes away. This is the optimal height in terms of signal strength.
- Next play passages across all 4 strings and listen to the volume balance between the E/A and the D/G strings. If the D/G strings seem lower in output, raise the treble side of the pickup slightly to compensate.
Now for the neck pickup. You have two choices here: you can solo the neck pickup and use the exact same procedure so the neck pickup is set for optimum signal strength without string pull. OR, if you tend to play a lot with both pickups on full, you can set the neck pickup to the position that yields the best blend between the two pickups as follows:
- Lower the neck pickup to a starting point that is obviously too low (like 1/4" lower than the bridge pickup)
- Turn both pickups on full and play a passage you are familiar with.
- Raise the neck pickup in small increments until you hear the best blend between neck and bridge (this is a matter of preference so it may not be 50/50)
- Once you've found the blend, play in the upper register on the E & A strings and make sure you don't have any string pull wobble sounds
- Now solo the neck pickup and play across all four strings listening for the E/A string volumes compared to the D/G volumes. Adjust the treble side of the pickup as needed.
- You're almost done: now that you've set your pickups just the way you like them take your handy ruler and measure the pickup height on the bass and treble side of each pickup and WRITE IT DOWN for future reference.