Hi S.,
YES, the Alimentum can make their poop runny. It is messy, but no big deal. Keep with it. Both of my kids had to use it, and for my daughter we mixed it with Soy because it was constipating, to help keep her more normal, but now research and my Pediatrician say that soy formula is bad because it mimics estrogen and can change the baby's hormones. So, don't go that route. I personally would say to keep with it and it should even out eventually.
Don't let the breastfeeding people get to you, both of my kids were allergic to my breast milk, and I couldn't make enough anyway, so I had to use formula too.
As for the baby acne, yes, this is very common on newborn faces, they are just getting rid of the extra stuff they don't need anymore. But, the butt, is another story. My babe ended up in the ER because his was so bad. (The advice nurse told me to take him.) We used 40% Desitin, the strong kind, 40% yeast med like the nystatin, and 20% hydrocortizone. It cleared him up in a couple of days. Mix them all up together and then put it on her every time you change her.
The baking soda baths are to neutralize any acid left on the skin. These should not be more than 10 minutes tops. I still use these for my kiddos and they are 3 and 5.
You are doing a good job mama! Keep going. The milk allergy will really get better as she gets all the protein out of her system.