If you want a flat side on the sheath, just put less foam on that side in the press. Could even go with no foam at all on one side, but you'll want a lot on the other side. I'd also put another peice of kydex (cold) or something in between the knife and the press as a liner so it doesn't get messed up if you go without foam.
Lately I've just been doing the wrap thing and letting both sides mold to the knife. Then I heat the belt loop up and mold it to match the contours of the knife and sheath. That way the side of the loop against the sheath matches its contours and then you just pull the other side of the loop out and square it up.
Thats a real nice job for no more kydex than you done though. Better than what I've been turning out, I'm getting tired of the stuff :barf: Gotta get some spare time and try leather.