Eczema is a tricky condition, and it can take a lot of trial and error to find the right mix of medications and sensitive-skin products to keep it in check. It's great that the rash is improving, but the patches on your son's cheeks should be treatable, so talk to your pediatrician to see if he is on the maximum treatment regimen. Or consult a dermatologist who might be aware of newer, more effective treatments.
It's not uncommon for some kids with visible eczema patches (like on the hands and face) to get teased or least questioned by other children. Teach your child about his condition and arm him with a standard comeback to other kids' curiosity, such as "Oh, that's just my eczema. I was born with it, but you can't catch it." If your son is being viciously teased, you may have to talk to his teacher so she can educate the class about what eczema is -- and that it doesn't mean your child is weird, bad, or sick. Children are naturally curious but also generally accepting of what they understand.