Joel,
Post this same question on the NetFoos web site. Hugh has a mathematical system for handicapping that he uses in the Jacksonville tournaments. Its a random DYP, but depending on the points level of the teams involved in each match, one might give up every serve, one point per match, one point per game, etc. He can tell you the math.
We do high / low DYPs with good results in Charlotte. Players trust the Net Foos points system and the tournament director can always use discretion if new players join who are already strong. When in doubt between two middle players, always place the better forward in the top side of the DYP.
Designated doubles will tend to frustrate your better players who want play forward. Instead, the Roto format is a blast. It creates some team tension when a good forward can't make a block or score from the back in order to get back up front and his partner can't score from the 3 bar either.
One final handicapped system is to limit forwards to one goal per type of shot per game. One wrist rocket, one pull , one pull kick, one push, one Euro pin, etc. If they shoot a second one, the ball goes over to the opponents goalie.
Good luck.