Sorry I came to this thread late. I was doing a search on "secondary burn" and came across this. I'll respond here since the link referenced above to the thread wahoowad started is from the beginning of the year.
I had my insert installed on Friday, and just stopped in the stove shop to talk to them about my experiences so far. Wanted to see if they thought I was doing things right. It turns out, from what they said, I didn't fully understand the secondary burn, and might have been doing things wrong.
My insert has a bypass (to the flue) on it and an air control. I had thought that to get secondary burn I needed to 1) have the air control wide open so air was blowing into the firebox, and 2) the bypass closed.
What I was told today (which jives with something said in the thread linked to above) is that actually the air control doesn't control how much air is entering the system, but where the air goes. To get a secondary burn, the control has to part or all the way closed so that the air entering the stove is re-directed into the burn tubes (I think) thus initiating the secondary burn. By keeping the air control all the way open, I was just blowing the air into the stove and thus not getting secondary burn.
I was told the bypass does not affect secondary burn at all. I thought if it was open, all the smoke and gasses would exit right up the flue, and therefore there would be nothing to burn in the secondary burn. Apparently this is not the case.
Also, the secondary burn does not ocurr just up in the baffles near the burn tube holes, but will occur everywhere in the firebox.
I'm going to give this a try as soon as the weather cools down again and see how it works.