I had to lower the pickups on my 4003 because they are too hot. I back the tone all the way off on the neck pickup and almost (80%) all the way off on the bridge pickup. By using just the volume controls it has so many useful in between tones, it's unbelievable. Had a horrible time trying to balance the pickups on a fretless jazz, though. No matter what I did it seemed to get worse. I guess it depends on what you're trying to achieve. The higher the pickup, the louder and more bass frequencies will be produced, lower the pickup, and it gets softer in volume and brighter in tone. This may help if you want to accentuate the heavy bass with a raised bass pickup matched to a lower bridge pickup to add some sparkle to the top, or the other way around to get a bright, punchy sound from a high bridge, and a bit of grunt from the front.
