My DD had some real bouts with nasty diaper rash, having inherited her mother's sensitive skin.
Here was our biggest secret: a liquid antacid like Maalox or Mylanta. Use a cotton ball (or 2) soaked in the liquid and coat his bottom with it after you've cleaned him after changing. The antacid counteracts the acidic components of urine and feces and makes the skin feel better. Sounds weird I know but I swear it works.
We'd usually let the mylanta dry, then put a little powder over it to make sure it was dry, then apply diaper rash creme over that, then lightly powder that to keep it from sticking so badly to the diaper. Sounds like a major production, I know, but 1 or 2 changes using this routine and she'd be considerably better.
We've used Balmex and A&D both and they're both good. Weleda diaper rash creme is great, and actually has a higher zinc oxide content than most of the other brands. Sometimes if one brand isn't working, another brand will. Consequently we used to keep several on hand, bringing out the Weleda if things got bad.
If the rash is caused by yeast, I would use an OTC yeast preparation like Monistat or GyneLotrimin creme. My DD never had yeast diaper rash so I can't offer much there.
Of course you know all the other stuff about frequent changes, letting air get to his bottom, cleaning as much as possible with water, that kind of stuff. Pampers Rash Guard baby wipes really do help too.
You might also need to change the kind of diaper you're using. My nephew would develop terrible diaper rash unless his mom used Pampers. My DD did better with Huggies. And some kids are better in cloth. But if you're using a store brand diaper, you might want to try a premium brand and see if they keep more urine away from his skin.
Please let us know how it goes.