Myself and my partner went and picked up our German Shepherd puppy the Friday just gone and we are having problems getting him to eat his meals. Some days he will eat his breakfast and not eat his dinner and vise versa, and there has been a day where he hasn't eaten anything.

We are trying to feed him the same as what the breeder was, 1 cup of dry food with 3/4 of a cup of mince watered down and it doesn't seem to be working all the time.

He has had an upset stomach for the past couple of days, is that and the combination of being in a new environment effecting his eating?

Did you get vaccination certificates/card with him to show what shots he has had?

Odds are he is just settling in to his new home, it can takes weeks up to months for a dog to fully adjust to its new surroundings.
With a new pup you have to remember, it has just gone from being around all its brothers, sisters and mother to being 'alone' with strange people.

Have you tried puppy milk for him just to make sure his fluid intake is kept up?