How i set up pick up height in my RGs :
1. Tune/Intonate/Set the action - you want it to be steady and easy as possible
2. Plug in straight to the amp, get the best cable you can use while youre at it.
3. Set everything @ 12' oclock, both clean and dirty channel. So you can determine the guitar's "raw" sound.
4. Set the pickup height high then work your way down,(of course you need to balance the pickup volume or output first,it doesnt matter if you set the bridge or neck first,it really depends which one youre using the most)metal players usually leave it high enough for compression but ideally,you want the pickups to perform at their best. Too low=less compression,less attack,less bass but it sounds clearer. Too high= muddy,bassy,more compressed. Sustain/string feel(youll notice that guitar will get more "acoustic" feel to it once you lower down the pickups,lower means less to no magnetic pull from the pickups) really depends on the pickup height,too high will pull the strings and too low will kill the signal.
To sum it up,just use your ears. This is how i setup mine.