It's really unusual for a puppy to pee/poop in it's crate, they usually don't like to soil their sleeping quarters. Absolutely the feeding schedule, but that in itself is very dodgy with such a tiny young baby.
Obviously I don't know how big the crate is (!) but wondering if it's big enough to put it's bed at one end and the pee pad at the other? Better still if the pee pad has been slightly peed on previously, so it has some kind of a clue what to do on it!!
Sally + Harry x