Pickups out of Pase... or what?

As most of you probably know, I just recently completed installing 2 Seymour Duncan HB's on my Ibanez. I've been playing using them so much that I negleglected the center pickup. I noticed that by itself the Center pickup sounds like it always has (liek a stock Ibanez pickup), but when the switch is set so it is "live" with eaither of the HB's the tone is realy crappy, and quiet, and has a lot of noise. Can I fix this just by making the Green wire the hot wire and grounding the black or do I have to flip a magnet on each of my hb's? I don't realy feel like taking the Bastards back out after I finaly got my Damn Floyd Rose bridge working right :evil: :evil: :!: :!: