The timer is just a set of contacts that are closed when wound, and open after a set amount of time. The thermostat is just a set of contacts that close when it calls for heat, and open the rest of the time. The override switch is just a set of contacts that are closed by your finger when adding wood, and opened by your finger when you're done.
All three are wired in parallel and any of them closed, will open the draft. You could have 50 sets of contacts if you wanted to and if any 1 of those 50 contacts closed, the draft would open. Page 58 of the manual shows the wiring diagram.
Stupid statement ... but everyone has read the manual and knows the firebox needs to be heated back up after loading or the secondary combustion doesn't work right? If you shut down the draft override, and you don't have flames above the fire, you need more time with the draft open or it's just going to smoke like crazy.
For the reason stated above, I run full (I mean full!) loads of wood and try to complete a full burn cycle (6 hrs+) before adding more wood. Secondaries will stop holding flames as the wood burns down as most of the gasses have been driven off and burned by then. As stated before, I am burning dry, but low quality ash and elm.