My daughter also has a rash under her neck (from dribble and milk running under there). I'm not sure of any natural remedies. I just try to keep under her neck as dry as possible. When i bath her i pull her head back a bit so i can gain access to that area, and give it a good sponge down, again making sure you thoroughly dry the area afterwards. I do the same in the mornings over the bathroom basin.
You could try some pinetarsal, and sponge him with a bit of that, i'm not to sure how natural it is though, you would need to check with your pharmacy.
I have found since the weather has cooled down a little, my daughter's rash has eased off a bit.
Your local health food store could probably recommend something, they have a great range for babies rashes etc.
Have you tried doing a search for natural remedies on the net??
Mel, mum of Joshua 8, Maddison 5, Hailey 5 mths