Hang in there! Keep up with the meds and try to wash everything in HOT that comes in contact with the thrush areas on you or the baby....including your shirts, bras, towels, everything! Use only liquid soaps as yeast can live on the bar soaps. Try to go without hand towels until it's clear...use disposable paper towels. Disposable nursing pads are best too, but change often so nothing breeds. A lot of open air time does wonders too.
As for schedules....I would avoid the book 'Baby-Wise' and any other baby-training books like the plague! As most lactation consultants and nursing mothers will say....it can be the doom of a successful breastfeeding relationship, as well as just cause confusion to a newborn babies natural time clock. Babies eat when they are hungry, not because they can tell time. Every baby is different....some eat every hour or 1 1/2 hrs, some eat every 3 hours and all babies go through changes such as growth spurts and developmental changes that have them eating more often or less often many times in their first 2 years. The best way to bond with your little one and to nurse when they will really need it most is to listen to them and get to know them. Let your baby lead you and tell you when he needs something, not a stopwatch. Baby-trainers that write these books are misleading new moms into following these schedules, clocks, charts and books rather that just watching and learning about each other and providing what each other needs.... right now your baby needs to nurse on demand (whenever he is rooting, sucking, crying) anytime of the day or night. If you ignore his signs and only allow him to eat based on a stopwatch he will stop following his own bodily signals and lose confidence in his own knowledge and in his caretakers.... Unfortunatley that crazy book is always right out in front in most baby sections, very sad. I would HIGHLY recommend the books by Dr Sears instead, check them out! Just feed your baby whenever he wants....geesh, my 1st nursed every 1 1/2 hrs for the whole first year....my pediatrician says that she just has a high metabolism. I can't imagine what I would have put her through if I had forced her to wait 2.5-3 hrs for her next meal. I don't think it's healthy for anyone, baby, kid or adult to only eat on a schedule and most health care providers and nutritionists say eating many meals rather that fewer bigger meals is healthier....
Hang in there, this will pass, you can do it. Love on your little one and let him nurse whenever he wants :-)