At the very first onset of a bit of a runny nose, I would give your child (I do this with mine) something called, Emergen-C. It's a fizzy powder drink mix that you mix with water or whatever. Each packet has 1000mg of Vitamin C. I put 2 packages in a 9oz sippy cup and give it to mine. The runny nose stays away as long as I give 2 packets in a sippy cup daily. It's wonderful stuff! You can get it at Wal Mart or a health food store. Wal Mart has just a few flavors, but there are more at the health food store. You can get the Super Orange at Wal Mart and that is what we use. There are Pink Lemonade, Cranberry, Raspberry, Tangerine, etc.
Anyway, Vitamin C also boosts the immune system as well as reduce the inflammation (colds).
Other things that I have done with my kids (we are hardly ever sick) is give them an immune booster when the first onset of sore throat and it's gone by the next day. We pretty much get all of our stuff at the health food store. I usually open up the capsule and put it in orange juice for the little ones. We use the NOW brand of Beta Glucan which has 100mg of Beta Glucan and 160mg of Maitake Mushrooms in it.
Another great thing to have around the house is (well there are more, I could write a book.lol) some probiotics. This will put the good back in the body and help him fight off what he has. If it's an ear infection or even just pain, an herbal formula called Ear and Nerve found at www.herbsfirst.com is wonderful!
But honestly, I would get to Wal Mart and get the Emergen-C. It's in a box in the vitamin section. It will take a bit to get caught up with your son, but keep it going. Catching anything early on is much easier to remedy than when it gets worse.
Good luck!