I think anywhere is better than not having a flusher. I have a Tornado and I think closing the valve and putting in 3-5 gallons gets more out than just running the flusher with the valve open.
I use a clear 3" extension so I can keep an eye on the flow. If I open the valve with the flusher on and wait for the tank to empty then wait and watch, it looks like everything is out and clear water is flowing out. Close the valve and fill for 5 minutes, then open the valve and a couple more piles of TP and stuff comes out. It usually takes 2-3 cycles before nothing comes out.