You mentioned you want them slightly different heights, is there a specific one you want to be higher than the other?
Currently I'm printing with my right extruder (Which according to the FF instructions is the one you're meant to use when levelling the bed) but the left nozzle is definitely is very VERY slightly lower and keeps catching my prints. Only very lightly, but it's enough to pull the odd bit off the bed if it's not stuck down well.
Is this that the nozzle is out of whack or my levels or my settings, or just that my adhesion isn't good enough?