I like an evenly balanced pickup so I usually set my pole pieces to roughly match the fretboard curvature.
I use 12-52s with a wound G so I set the G higher, the B quite low and the E a little higher. With a plain G string I believe it would be the D high the G low.
To fine tune them I use the input VU meter on my space echo and my ears
As far as pickup body heights go. If it's the standard filtertron mount (ie mounted to the top and or braces) then I would shim the bridge pickup so it is producing roughly the same amount of output as the neck. generally the bridge pickup needs to raised a bit, you can use foam, mouse pad, wood shims whathaveyou. I typically use more solid material as I like the idea of the pickup being firmly mounted to the top and potentially picking up body sound via the pickup being microphonic (and they all are a little)
I have adjusted a few vintage filtertron equipped Gretsch's. I believe TV JOnes modelled his pickups after the vintage ones.
I'll put up a picture of my Deluxe Chet's setup (It's the only filtertron gretsch I currently have). It has filtertrons (albeit with one role of poles removed) and as it's a 72 it has the advantage of the filtertrons being English mount and easily adustable for pickup height. Still you can kind of see the setup
I believe people that want a fatter more aggressive sound (rock) have the pickups and pole pieces close to the strings.
people that want a cleaner less fat sound keep the pickups farther away and raise the pole pieces.
I tend to play completely clean and use pedals for distortion. This sort of setup works fine for that, for me.
I would experiment and see what you like. It's all relatively easy stuff and you can't wreck anything adjusting them, unless you use a hammer...
As these have metal pole pieces rather than magnets one can get them closer to the strings without the pickups magnetism affecting sustain etc.

