H.V.
I had concerns about soy-based formulas, too. I primarily breastfeed my son but have had to supplement with 6 oz of formula a day. He, too, has had significant problems with gas. I eliminated dairy from my diet, which helped somewhat. Our pediatrician recommended that we use Enfamil's Nutramigen for the supplement. It has extensively broken down milk protein and is essentially hypoallergenic (Similac's Alimentum is the same thing). It's more expensive than regular formulas but in our case it truly helped curb the gas issues.
Good luck - I know it isn't an easy decision to do this!