I would have to disagree about prime not being able to "find" the new water. It's a chemical reaction that takes place - the prime molecules are in fact looking for ammonia molecules to bond with. If the water conditioner is added while the tank is being refilled, it will get mixed just fine.
Besides, prime doesn't detox water - it detoxes ammonia, nitrite, chlorine, chloramine, heavy metals, ect. There is an amount of each of those things that one dosage will handle. Whether the water is old or new is irrelevant. The only issue would be is if the volume of new water contains 7ppm of chlormine and it only detoxes 5ppm, as an example.
How much prime is needed is entirely dependent on the amount of toxins that are in the water.