i have to say i didn't know from experience, but i have two ideas for you. try this:
In the speed tab after you click configure, pick the PWM unit that controls the fan you want to use and click the automatically variated box at the bottom. In the temp tab, where it says "desired," pick the temp you would like. I assume the lower you pick the more it will increase fan speed. On the main window of the program click "automatic fan speed" under the configure button.
there is also an events section where you can tell speedfan to do certain things at certain temperatures. It seems too primative to control a fan speed, but in a discussion of that feature the author said he would like feedback. It might be worth contacting him to see if he could add that control in.