Here's what i do when i get ESP guitars with EMG actives :
1.) Press and hold high e (string #1) at last fret
2.) Adjust that side of pickup to 4/64in from bottom of string to top of pickup
3.) Press and hold low E (string #6) at last fret
4.) Adjust that side of pickup to 6/64in from bottom of string to top of pickup
Height difference doesn't make any tonal difference on active pickups, by the way.