You will want to be as high as possible for visibility, especially when taxiing, yet you will want to leave some clearance for turbulence. I highly recommend installing a crotch strap for your harness, that way you can cinch it down and prevent yourself from being bounced up into the canopy.
In determining my seat cushion height I got everything in place and put on my headphones. We adjusted the thickness to yield about one finger thickness between the top of the headset and and the plexi. I suspected the seat cushions would compress somewhat and that is exactly what happened... I now have nearly two fingers clearance. Overall, it's perfect. I only occasionally bounce my head into the canopy, and if I've really cinched down my crotch and lap belt then I don't hit it at all.