When I choose to close the bypass damper and begin backing down the air depends mainly on the wood species and the size of the load. With dry pine, I can close the bypass anywhere from about 250F to 350F on the stovetop and have active, secondary combustion right away. As long as the secondaries maintain themselves for a minute or so after shutting the bypass, I then close the primary air about 1/3 to 1/2.
If I am using a full load of oak, for example, I usually have to get the stovetop get to around 400F to 450F before I close the bypass and begin throttling back.
I've found the ash lip on the stove body and the "spring" on the air control make a good, general guide. Take a look at the "spring handle" on the control rod. The first 3 or 4 coils touch one another. Then the spring opens up into coils that have about a 1/2" gap or so between them. Standing over the ash lip on the stove, looking straight down, I push the rod in until the entire spring is visible when I make my first "real" adjustment to the secondaries (the first adjustment of closing the air 1/3 to 1/2 mention above is just to keep the stove from going nuclear with dry wood). Again, as long as the secondaries are still strong, my next adjustment is to push the 3 or 4 coils of the spring that physically touch one another "under" the ash lip, leaving only the "spaced" coils visible when looking down.
My final adjustment usually ends up pushing 2 or 3 of the "spaced" coils "under" the ash lip so they are no longer visible (again, this is standing over the ash lip looking straight down). You'll experiment and find the sweet spot with your stove. For example, you may be able to fully close the air control on your stove and still maintain active, visible combustion with no emissions. My stove simply refuses to do so, and I have to leave the control open about 1/4" to maintain a clean, active burn.
I make the above adjustments over a 15-20 minute period, depending on how the fire behaves. My stove likes to cruise anywhere from 600F to 700F during strong secondary combustion.