Bass Guitar Neck Setup: Intonation & Pickup Adjustments
Intonation is essentially having the string exactly in tune, not only in the open tuning, but fretted at it's octave, the twelfth fret. All you will need for this is an accurate tuner and the correct tool for saddle length adjustments - usually a small screwdriver or allen wrench.
Adjust your pickups so that they are at a point where they won't get sanded down from contact with the strings, yet aren't so far away that they lose volume. Be careful though, that you don't put the pickups so close that the magnets in them pull on the strings, damping out the sustain. The thicker your strings are, the closer the pickups can be because of the higher tension that thick strings have.
Well, now you have it. Keep records of the measurements and play your bass for a while and see if there is something you want to change. If you want to change it, why not, GO FOR IT! Only YOU really know how you like your bass set up, so why not do it yourself. As long as you don't try major surgery on your instrument, it is very hard to cause serious damage. The most important thing is to keep your truss rod tightened enough that it prevents warping. Don't ever leave the truss rod nut completely loosened! You should pretty much follow the order of the adjustments that I followed, because the subsequent ones depend upon the previous ones to work right.
Dan Erlewine's book, The Guitar Player Repair Guide.