My twins had the same experience - I was nursing and had to supplement since I was feeding two babies and they weren't gaining weight, part of the time their poop would be the yellow, seedy breastmilk poop & others it would be the green poop that is attributed to formula. According to our pediatrician, if it is not watery and there is no mucus, you are fine. Once they were solely on formula, they would still have the yellow, seedy poop several times a week and when I asked our pediatrician about it, she said that the quality of formulas have come so far that they often produce the same poops that breastmilk does.
All three of my kids had problems with gas - the nurse in the hospital when my daughter was born told us to put a warm compress or even a warm washcloth on her tummy and then swaddle her - it was amazing! Within 5 minutes of doing this, she would start to pass her gas and you could just see her relaxing - it worked with the twins as well. I just bought some kid-sized ice packs that could also be warmed and warm them in hot water for about 2-3 minutes and it did the trick! There are also several websites with 'exercises' you can do with your babies' legs to help them dispel the gas.
Good luck to you and congratulations on the birth of your son!