She is on a soy based formula,(Isomil) after being switched to a low iron Enfamil that did no good. She did well on the Soy for a while, but then i started in again. And with the Applesauce, it makes her go about 2 or 3 times a day, but its hard

Applesauce is like Pedialite (you can give it to your child for dehydration of you can use it if they have diarreah) Applesauce could constipate or do the opposite.I guess it depends on the child.
I havent tried Prunes yet, I want to make sure shes going to have no reaction to the Applesauce before trying anything new.
As for the Karo, shes been on it for more than a month, and it hasnt even come close to helping her.