I'm so sorry you and your little one are going through this.
My son went through this when he was just a few months old and his pediatrician recommended we use cortaid with vaseline over it. I've also used Desitin with corn starch powder as well and both seem to do the trick.
If the diarrhea doesn't wake her, I wouldn't wake her up. If she isn't feeling great to start with, she probably needs her rest and I wouldn't risk not being able to get her back down.
Wouldn't hurt to let the area open to the air a bit during the day when she is awake and just playing, just cover her lightly with a towel or blanket.