It is important to have the pick-ups sitting properly under the strings for best sound and output. The trick is to adjust them so they are not too close and not too far away.
If the pick-up is too far away from the strings, it will have weak output or not much volume and tone.
If the pick-ups are too close, the strings may rattle against them. Or the magnets of the pick-ups may pull the string out of its natural orbit as it vibrates. This causes a funny out- of- tune sound. This is particularly true with very light gauge strings.
Adjusting the pick-ups up and down is a simple matter of turning the one or two set screws that sit on each side of the pick-up. (See Fig. #1) Adjust them from 1/8th to 1/4 of an inch under the string. Be sure that after you have made the adjustment, you hold all the strings down on the last fret of the neck to see if you are hitting the pick-ups. If all looks good, play the instrument through an amp and check the output. Re-adjust as needed.
On some pick-ups you will notice one or two individual set screws under each string. These allow you to adjust the output of each string separately. (See Fig. #1)
This need only be done when you feel that an individual string is not coming through as loudly as the others. If this is the case, bring the set screw for that string up closer to the string. Or, if you feel one or more strings are too loud, lower the screws away from those strings. These adjustments should then balance the output of all the strings. If there seems to be major differences, have your local repairperson look at this for you.