my little one had thrush recently, both in her mouth and on her bum, I think. I used clotrimazole and also used something which is often recommended as a natural alternative, which is citricidal grapefruit seed extract. I bought it online in a small bottle and I just added about 20 drops to 2oz of water, and dipped cotton wool into it to wipe her bum over.
Also, some suggest using this stuff (it's only a natural vegetarian food supplement) in the initial rinse (I just pop the drops into the prewash section) when you wash your nappies, but quite a few drops (say, 70), and this will help to kill any yeast lurking in the nappies. The idea is that the GSE kills fungus and bacteria, so I did this the other day. I've had no problems with rash on her bum since treatment started.