pickups heights are quite subjective...

usuali the bridge pups are higher
and the neck pups are lower...
jz make sure the notes sound same loud on both pups

for me...
usuali the bass side pup is lower than treble side...
just to make sure the lower notes dun overpower the higher tunes
and so tat ur pups magnetic field dun disturb ur string vibration and kill sustain

usuali pickups wit cover can go closer to the strings
since covered pups produce a large area forcefielf
instead of concentrated magnetic field as the polepiece siblings