I am sorry to hear about your problems with Amber. My name is Rebecca. I am a veterinarian and will do my best to help.
Is her poop normal in color and consistency or is it soft, runny, or overly hard and dry?
What is she eating?
She may be pooping more than normal, but growing puppies do poop more often than adult dogs. Have you had a stool sample checked micorscopically for the presence of parasites, blood cells, mucus, etc.?
If she can hold it in her crate, then perhaps she needs more crate training before being allowed free run of the house.
Where in the house does she poop? Any particular type of surface such as carpet or tile, or any particular room? If she is going in particular spot or on a particular surface, you cold try using baby gates to keep her off these areas.
Let me know what other questions I can answer.