My puppy is sick, he is vomitting yellow (same color a pee)he drinks but then throws it all back up. Has lost his appetite. This morning he pooped dark brown and watery and it smelled rotten.

You're puppy more than likely has parvo.

You need to contact a vet immediately. Parvo will kill your dog without the correct type of treatment.

Ditto, It sounds likely that parvo is the problem.
Puppies can go downhill very fast, so best to get him to vet ASAP.