Hey Paul. I found this article describing three "generations" of synchronous rectification techniques. Likely you'll want to start out with the first generation - calculate the expected turn-off time of your drive mosfets, give it a little space, then turn on the rectifying mosfets. It has some inherant flaws (anything that simple has to have flaws), but it will be a major improvement over diodes. Seems to me that leaving the diodes in place is not a bad idea anyway.
Give it a read-over just so you're aware of the other techniques in case you want to jump on them. Not sure if your ATM8 is going to handle the advanced techniques.
Predictive Control Maximizes Synchronous Rectifier Efficiency