I don't know when the best time is to set your vent baffle. I've been running mine fully open and simply varying the motor speed to give me the optimum draft. So I can't answer that one.
As far as running a rheostat vs. using the baffle for draft control, I think the rheostat is better. Running the motor at full speed and then restricting the air flow with the baffle creates unnecessary turbulence in the vent system. Not a good idea with flyash in the vent. Using the rheostat allows me to slow the motor down, smoothing out the air flow, reduces the amount of flyash picked up, reduces the sound level of the direct vent system and allows me to easily adjust the draft as needed.
It's interesting that on page 2, item 16 of the old Keystoker Koker direct vent operating instructions it states "On all top vent direct vent models, the exhaust motor is equipped with a rheostat." So apparently this used to be a standard feature.
I hope one of the other guys can help you with your question about when to adjust your vent baffle.
Also, I wouldn't hesitate to call Keystoker. They've always been very helpful when I've talked to them.