They will keep breeding as long as you take the eggs.
You will only ever be able to get one egg at a time. If you don't collect an egg, the Pokemon won't continue breeding until you accept or reject the egg.
You can have one Pokemon in the Daycare for as long as you like, then put another compatible Pokemon with it and they will breed. You don't need to withdraw both Pokemon to make them breed again, just put the one you want to breed together with the one already in the Daycare.
