Ok here it goes. I had the longest, worst case of thrush with my 3rd.
You can make your own solution of half vinegar half water and put it on your nipples after nursing.
Make sure you stay as dry as possible.
You can also make your own nipple cream with antibacterial/anti-fungal and something else which escapes me at the moment but I can send you the mixture via email.
Oh I also got some VSL#3 I think it is called. It is a probiotic sold at peoples pharmacy. It made me feel immensely better.
You can treat yourself and the baby with nystatin, diflucan or gentian violet. It seems as though Nystatin might not be as effective as it used to be. Sometimes I just debated going straight to gentian violet.
If you have a mild case any of those should help. But if it is a bad case that is more persistent you can find some great information at: http://www.breastfeedingonline.com/newman.shtml
Good Luck!
J.