The string is the signal source for the pickup. Pickups produce a magnetic field that is altered by the vibration of the string, thus creating the electrical signal that becomes the sound of your guitar.  You will get the best and fullest tone by setting your pickups as close to the strings (signal source) as possible without physical or sonic interference.

Physical interference happens when the string hits the pickup. The string colliding with the pickup will cause a popping sound. Your pickup should be lowered just far enough to eliminate any popping sound that may occur during aggressive playing.

Sonic interference also tells you that the string is too close to the pickup. "Stratitis" is a made up term to describe the "warbling" sound that is produced when a single coil pickup is set to close to a string. Stratitis is most commonly produced by the neck position pickup on the Low E string because the the string will move and vibrate most close to the neck. In addition, the Low E string contains the most metal and will be most affected by magnetism. 

You may hear this multi-tone or warbling sound if the pickup is too close to the string. Fret the low E string at the 12th fret and listen for it. If you do not hear it raise the pickup until you do. Then lower the pickup slowly until it just disappears and you get a clean, pure single tone. That is where you want it.

Your middle pickup can be closer to the string than the neck pickup and the bridge pickup can be closer still. That is because the string gets tighter towards the bridge and is less affected by the magnetic field of the pickup.

Typically humbuckers and P-90's with bar magnets under the coils do not have stratitis. It mainly applies to single coils with actual magnet polepieces. However it is these magnet polepiece type pickups that produce the clear, natural and glassy tones that we all love so much.

Rio Grande also offers many "true splitting" humbuckers with magnet polepieces. These include the Muy Grande, Halfbreed, Tallboy, and Babybucker series of pickups, as well as our entire line up of bass pickups.

LASTLY, experimentation is key.  Pickups can and should be adjusted to suit the needs of the player.  Often times we set the bridge pickup height for the best tone, then adjust the neck position to blend best when combinations of pickups are used.