Guitar Pickup Adjustment Basics:
The basic start point for Stratocasters (see end of page below for humbuckers) would be the Fender recommendations of distance between the underside of the strings (held down at the highest fret - 21 /22 etc) and the top of the pup pole pieces;
> Bass E side 5/64" and Treble E side 4/64" (for standard single coil pups)
> Bass E side 6/64" and Treble E side 5/64" (for vintage style single coil pups)
If you have read the Guitar Pickups Explained page of this site you will realise that a 'one size fits all' measurement is not going to be optimum. Due to the differing relative sizes of string vibration, the Neck is the pup that will get the largest amount of magnetic coupling and the Bridge the least i.e. it would be natural for the Bridge pup to have a lower output that the Neck pup from the same string vibrating above them.
A recommended adjustment routine (assuming a balanced vintage tone 'target') would be;
> Set all of the pups level with the scratchplate (i.e. not higher on the top or bottom E side).
> Adjust all 3 pups to the sort of distance quoted above, do not be too precise at this point. Remember that the same number of screw turns are needed each side of a pup to keep it level.
> Start with the Neck pup; play your favourite pieces across all 6 strings including some very high fret work and see how it sounds. There should be no string / pup collisions even with hard picking. If all is well try edging the pup a bit closer to the strings (still flat for now) until you get problems - either the sound starts to deteriorate to your taste, or a string crash starts. As things start to go wrong, back off the height a little until things sound as you want. Keep the pup flat for now.
> Do the same thing with the Middle pickup, which you will probably find ends up with a slightly smaller gap than the Neck.
> Now try playing and switching between the Neck and Middle. The volume should be very similar. If not, the louder one need to be lowered a little (you should not raise the quieter one as that would negate the earlier steps of course).
> And finally use the same techniques on the Bridge pup - initially on its own as before. This is likely to end up with an even smaller gap than the other 2.
> Now try playing and switching between the Bridge and the other 2. This is a very personal step because different players like the bridge to have different (normally more!) strength to the other 2 pups and the number of Neck pup windings (compared to the other 2) is a key differentiator between pickups styles.
> As before, its the pups that are too loud that need to be lowered. Do a final check across all 3 pups to ensure relative volumes are established. Remember that the Middle and Neck were balanced in the previous steps, so if one of them is being lowered the other probably should be too!
> Now go through each individual pup and check its bass to treble balance. If you feel a pup needs less bass, lower the bass end slightly etc. These should be small tweaks so as not to disturb the balance from all of the previous steps! If you want to really skew a pup towards either bass or treble, you can always do a 'tilt' i.e. bring one side up by the same number of turns that the other side is lowered - taking care of that overall balance again.
So that should have you done. Each pup is balanced in terms of individual tone and all 3 are volume matched.
If you still have the will to live(!) you can also experiment with the overall guitar tone. To do this all 3 pups need to be lowered by exactly the same number of screw turns on each of the 6 screws - keep a note of how many. This step allows the overall tonal 'shade' to move from 'percussive' towards 'mellow'.
So long as you know how to get back to the balanced state of the previous steps, there is no right or wrong here - its whatever Rocks your Boat!
And if the humbuckers have adjustable pole pieces, they too can be used to alter the tonal response (as well as matching to the fretboard / string radius in terms of individual string relative volumes). The key here is to do the basic tilting element first to get somewhere close to what you want. Then, assuming you are happy with the overall string volume balance, try screwing the poles up - do it the same amount on all of the 6 pole screws and try between 1 and 3 complete turns noting somewhere what you are doing. Raising the pole pieces while keeping the pup height constant has quite a dramatic effect on raising the brightness and percussive edge on naturally dark humbuckers.