Setting the min. speed for that fan to 1% and the fanspeed increment in the general options to 1(% steps) and having Set fans to 100% unchecked should work..
That should set the fan to 1% as soon as SpeedFan is started, if that's too low to get the fan started it probably gets hot in there and then the fanspeed starts to increase and the fan should start sooner or later.
When Speedfan is then closed it should stay at whatever speed is set right now and if you've given it some time to cool your system down and go back down to 1%(your min. speed) that should be the speed it keeps without Speedfan running.
This relies on the fact that you have disabled AutoGuardian in BIOS since that seems to take over control when SpeedFan closes down.