Poor guy!! It's so hard when these things happen. I can tell you what my pediatrician recommended when my son had to go on antibiotics. She said to get the probiotic complex at Trader Joe's, (don't know if you have them near you) and crush the pills and put them in his cereal or other food. It has a sweetish taste to it. It puts the flora or helpful bacteria, back into his gut. The meds destroy it while destroying the harmful bacteria infecting him. My husband also takes it as part of his regimine to control IBS (irritable bowel syndrome). I also put Aveeno oatmeal treatments in his bath water to help soothe his skin. You can get those at any drug store. And finally, I found that the best diaper rash treatment for my son was Butt Paste, which is available just about everywhere. It has a higher concentration of zinc oxide. You are doing the right thing by giving him as much "air time" as possible. When he's done with his med cycle, you may want to make sure he's getting yogurt everyday as it also replenishes intestinal flora, and possibly a green drink (dilute it for his age), like Green Machine. Careful with the green drinks as they can loosen the stools again. Thinking about it, you may want to talk to his pediatricain before adding too much to his diet.
Hope he gets better soon. Sending cyber hugs. B