The fan you run via molex to PSU is going to run at 100% full-time. Nothing wrong with that if you don't mind. If you want to maintain control of the fan, you can just get a fan splitter and connect two fans to one header. Not ideal, but it will work fine.
Edit: There are lots of choices for brands and prices, but you'll be looking for something like this: http://www.newegg.com/Product/Product.aspx?Item=N82E16812119148&cm_re=fan_splitter_3_pin-_-12-119-148-_-Product