Ok first off what are you being treated with? If its nystatin, it contains sugar and yeast (thrush) actually thrives off of sugar, so I'd not take that.
Go to the pharmacy and get Acidophilus caplets (teh kind you can break open) and Gentian Violet. You yourself take two acidophilus caplets three times a day, and break one open and rub in your babys mouth so she can swallow some. Its a probiotic, or good bacteria, and it'll fight the thrush off and balance out your flora so your body can easier fight off thrush. Then take the Gentian Violet, and dip a q-tip in it, and rubi t all over your babies mouth, its bright purple so it'll be quite the sight, but paint everything in her mouth, her gums, insides of her cheeks, top and bottom of her tongue, and roof of her mouth. THen take a NEW q-tip and do the same with one of your nipples, then a NEW q-tip again and do your other nipple, all around the areola and nipple.
This has taken care of thrush for us 3 times with both my boys. Like I said the nystatin contains sugar and yeast thrives on sugar, so try to cut it out of your diet too for a short time.
As for the sore and cracked nipples, let them air out as much as possible so they can heal, and make sure her latch is good when yo uare nursing.
www.kellymom.com has detailed instructions on using Gentian Violet. Plase don't give up nursing, it will pass and you'll regret stopping, even if yo ustop nursing you stil have tobe treated for the thrush! Good luck, and don't hesitate to contact me if you have questions!