Is there any risk of running both the fan and furnace at the same time?
Looks like you have a gas furnace. If so the furnace will fire and preheat the chamber before the fan engages. This help dissipate any cold air in the ductwork before it blows into the conditioned space. 
On page 22, Note #12 of your schematics there is a 25 second delay for heating. For cooling there is only two seconds delay.
For heating, this would be CPU controlled once the proving switches are engaged. See drawings on page 22 look for LPS, LGPS and HPS. Sound like you are on the right track, just wait for the fan to cycle on.