My niece was a croupy baby. She'd cough until she threw up the congestion in her chest. It got better as she got older, but she'll still have some trouble once and awhile.
Get an air filter for his room. Cover his mattress and pillow with allergy covers. Use synthic sheets (less cotton the better). If you have carpeting you may want to change to hardwood (expensive but worth it). Remove all stuffed animals. Dust every nook and crany in his bedroom. Switch to hypoallergenic detergents, soaps, and shampoos. Limit the perfumes in the air. Here's the big one... keep him away from smokers.
Make sure he takes his medications regular, too.