From a cold-boot, Speed-Fan will load from a short-cut in the Startup folder. It will load with the saved parameter settings you make for it.
You can tweak SF so that it will hold the existing fan-speed(s) on program exit. So when you do a warm-reboot, and unless the reboot was done when fans were running full-throttle, it will go through the reboot sequence at the low-speed fan settings.