The relative heights between neck and bridge on a Jazz is very important. One you have each individual pickup balanced across the strings you can start comparing volume between the two pickups solo'd and then finally fine tune the balance to fix the 'center tone' where both pickups are on full (or, at lest, even) or at the center detent on a blend. I like to have the bridge stand just slightly ahead of the neck, volume-wise, to give it a slight edge. Once that relationship is set, I have a perfect Jazz bass bark and snarl and my blend behavior is perfect for me.
Get a screwdriver and go at it. There isn't a factory setting that you are going to mess up, its all arbitrary. Experiment.
Some pickups have smaller windows. The N3 pair on my fiver come alive but only at a height lower than the Fender recommendation.