Hi WF. I apologize, I haven't been on the boards for ages, so I don't really know your application, but I think the best way to think about these heaters is much like any other heater. You want to keep a minimum path between combustion and exhaust to ensure efficient operation. Once this is accounted for there is almost endless scenerios for how to extract heat off of it. You can make your "zones" or "loops" quite extensive as long as you afford yourself the option of switching back to a short path when needed.
To simplify, run two T's straight between the combustion and the exhaust with a damper between the Ts. From those Ts do whatever you want. You can open the damper to preheat the output chimney and then close the damper to extract heat through your loop. I'm sure there is a scientific calculation to figure out how to complicate the system and match a length of pipe to a stove diameter, but the aforementioned approached makes the most sense to me.