I'm sure there will be many opinions on this and no one "right" answer. But me and my babe battled thrush early on and in retrospect I am really glad that I did the natural remedies and avoided the prescription meds. My approach was to try the natural things first and if I wasn't seeing serious improvement in 2 weeks to go on the drugs. Luckily we were able to kick it naturally, but not everyone is able to do that and it takes a lot of perseverance and work to do it this way. For awhile there I felt like ALL I did was treat thrush! Between the herbal treatments--both topical and supplements--and washing everything in vinegar and boiling any plastic parts (pacis, bottles, pump parts), and cutting WAY back on sugar and white flour, it felt like yeast ruled our lives.
But we kicked it and it hasn't come back! We basically followed Dr Jack Newman's candida protocol, which you are probably aware of, but its here:
http://www.drjacknewman.com/help/Candida-Protocol.asp
The things that were key for us IMO were the GSE, taking a good probiotic, and reducing sugar intake. I have also heard (after the fact) that eating coconut oil is very good for helping to maintain a good gut flora (and therefor reducing yeast).
I would certainly avoid any treatments with Nystatin or the like (the topical yeast drugs) as it has been proven that thrush is resistant most of the time to this now (it has grown resistant as the drug use has increased). So I wouldn't bother with that at all. The Diflucan seems to be the only way to treat it drug wise and I would consider that a last resort! (Diflucan is a pill and treats yeast systemically not just locally.) If you want to hear more details about what I did please PM me or reply in this thread and I'd be happy to be more specific. Why do you think you have thrush besides the diaper rash? Do you have symptoms too?
p.s. we didn't have the yeasty diaper rash, but I would think it would respond well to a rinse of the GSE just as thrush on the nipples does. You can also make a solution with some tee tree oil in it which might help like this solution for cloth wipes:
This recipe works best for yeast diaper rashes. The vinegar and essential oils discourage yeast growth.
Soothing Baby Wipes
1/2 cup Distilled Water
1 teaspoon Vinegar
1/4 cup Aloe Vera Gel
1 tablespoon Calendula Oil
1 drop Lavender Essential Oil
1 drop Tea tree Essential Oil