Of course the best way would be to put the correct communicating stat with the furnace. That's how you maintain perfect temperature, which is the whole point of a modulating furnace.
If you must use a binary on/off stat, Tranes work like this:
When W1 calls, the unit goes to low fire, 40%, and stays there until the call satisfies. If it's really cold out, W1 cannot satisfy the call, then W2 second stage also calls. This starts a "ramp up" routine that increases output by 3% every minute(20 minutes until full output) If at any time W2 call drops out, it immediately goes back to 40%. The main blower fan matches speed to the burner output to maintain fairly consistent temp rise.