My son has very bad reflux also. When he was about 3 months old he started nursing and taking 2-3 ounces of formula every 45 min. to an hour, he was very fussy, and would spit up a lot. He was not gaining any weight, he had only gained 3 ounces in 2 months. The specialist put him on Prevacid and had us thicken his formula with 1 tablespoon of rice cereal for every ounce of formula. That made all the difference in the world! He rarely spits up anymore and is hardley ever fussy. The doctor told us that the Prevacid did nothing to stop him from refluxing but that it neutralizes the acid so it's not painful, and the rice cereal is what will keep him from actually spitting up all the way.
We also had him on Enfamil LactoFree and that helped a bunch. I was breastfeeding but I couldn't keep up my milk production since he was nursing so often. Before we found this formula we had tried regular Enfamil, Good Start, Prosobee, Simalac, Nutramagin, nothing helped but the Enfamil Lactofree. I tried to eliminate dairy from my diet with no change. Also I don't know if you are giving breast milk or not but the doctor also said that if I were to pump and put it in a bottle not to thicken it with rice cereal. She said not to do this because the breast milk will actually break down the rice cereal and it wouldn't even work, she said to use Thicket instead.
We had also tried a few other reflux medications that did not help like Axid and Zantac. Prevacid seemed to do the best. My son gets 1/2 of a pill, they disolve, we were told not to put it in water or anything in a bottle to give it to him because inevitably you are going to loose some of the medicine when you do that. Instead we take it and rub it on the inside of his cheek for a couple of seconds and that way he gets all that he is supposed to, plus we're not just giving him extra liquid to spit up before the medicine has a chance to work.
Once your baby starts to sit up on her own the reflux should improve some. I've been told that most babies "out grow it" by about a year or so, just because they are more mobile and their little bodies are maturing. My son also did not eat very well at all when I was gone even if it was just to the grocery store. In fact one day while I was at work he refused to eat the whole time! From then on I decided I needed to stay home and work. I don't know if your daughter is in daycare, but maybe right them out a list of all the things they need to be doing with your daughter like keeping her upright, burping her after a certain number of ounces...
I hope this helps you some, good luck.