I think you will have to expermient with your situation. If your furnace is dampered down too much, the plenium fan will not kick in. And when it does it may run only a few seconds and kick right back out again, because the fire isnt hot enough to keep the plenium fan running. For this reason you may want to keep your 3 speed fan on low for starting a fire, it helps get your furnace to operating temp. Then bump the fan to a higher setting after it warms up some.
I have a hard time regulating my furnace with the (stove) damper alone (not chimney damper). If it doesnt get enough air, again the plenium fan will not kick in, and when it does, again it will kick out after a little while. Too much air, the wood burns too fast. So I've found the combo works for me. I'll admit, my furnace does like a babysitter, but it does heat the house well.
Another thing you may want to consider if you are using a backdraft damper. That would be a seperate damper that goes on the 12" pipe that carries the warm air to your ductwork, (see manual for details). Which prevents air from another forced air unit, ie; furnace or AC, from backfeeding through your wood furnace. Make sure if you are using one, to keep it slightly open with a screw (again see manual), so the hot air can naturally rise off the surface of the furnace, or your plenium fan will cycle on and off, until you furnace finally gets good and hot enough to keep the plenium fan running.