I'm new to the wood furnance world - i apologize if my questions seem stupid, i am definitely not very educated about this stuff. What is the advantage of the separate ducts? That was actually going to be one of my next questions after I found a good furnace to purchase. I would like to avoid having returns and vents all over the place if possible so i was unsure if the separate ducts were a necessity or not.
There are several circumstances where your wood furnace is producing heat but not enough to maintain a comfortable temp. If your backup heat uses the same duct, you can't safely run them both at the same time. That's because the wood furnace needs to dump the heat it's creating and if the backup is running when the wood furnace wants to kick on you have a problem. Either open the ducts and let the two fans fight each other, hoping the fans don't burn up or worse, damage one of the heat exchangers.
Sure, you can do the dampers (BTW I have to use powered dampers ~$400), and at this point that's my only option, but it's far from ideal. I will watch it closely and add controllers and relays (~$200) to make the best of a bad situation, but YOU don't need to do that since you have a clean slate. By the way, the only way I can figure to make it work, even with the dampers and controllers, is to set the backup thermostat a few degrees below the desired house temp. That way the backup only comes on when the wood furnace is low on fuel so the two are less likely to be running simultaneously though it's inevitable they will to some extent. You sure wouldn't want the backup kicking on while your wood burner was mid-load and making a lot of heat but it would do just that if both were set at 70* on a cold day. Now when you come home from work your house is colder than you like because your wood furnace is down to a few coals and your backup is set to 65* to prevent the two from running simultaneously. I'm planning to program the thermometer on my backup heat to run at 65* until 4pm or so and then heat back up to 70* because by that point the furnace is down to a few coals.
If you had separate ducts, you would set your backup at the desired temp and the wood furnace would do what it can and the backup will keep your house comfortable. The other thing I would do if I were building from scratch is build a furnace room on the exterior wall of the house with an exterior door so all the mess stays contained. Mine is in the basement garage which is tolerable but I definitely would not want the mess within the basement.
In your position, you can -and absolutely should- add a second set of ducts even if it's just a simple setup that doesn't hit every room. Have it dump 1/3 in basement, 1/3 main floor, 1/3 upstairs in a central location if needed. Your backup heat will have a duct system and it can be used to distribute the heat using the blower if needed.
I'm not sure of your climate but when it gets really nasty here we have to switch to the gas furnace. The wood furnace would do 80% of the work if we could run both on those -30 wind chill days but instead it sits cold. Last billing cycle just a handful days of having the gas on cost $40.
