You are correct to question this.. the BB will indeed die without any ammonia in the water. I'd say the easiest way is to move the AC20 to the main tank if there are no fry and drain the fry tank. When you are ready to raise fry, fill the fry tank with water from the main tank and move the AC20 over.
I'm assuming that you have a larger main tank, 40G or bigger? This way the filling of the fry tank is the same as a normal water change to it. Perhaps even just fill it 50% from the main tank and 50% fresh. The reason is to give the BB something to process until the fry start making waste.
>> Jim C. <<