Hard to answer w/ limited info on your system ..... in general tho I have found the software that comes on the MoBo CD to be the best method of controlling fans. For example.... the Asus M6F has:
Two (2) PWM Fan Headers - CPU and CPU_OPT
Three (3) Variable Voltage Chassis Fan Headers - CHA_1 thru CHA_3
Three (3) Variable Voltage Optional Fan Headers - OPT_1 thru OPT_3
That's enuff on it's own to control 2 fans on ya CPU cooler on CPU, 2 more on whatever and 6 case fans and CHA_1 thru CHA_3
I use em as follows:
CPU and CPU_OPT control the two water pumps
CHA_1 => Fan PCB_1 => five (5) case fans
CHA_2 => Fan PCB_2 => six (6) radiator fans in XT45-420 rad
CHA_3 => Fan PCB_2 => four (4) radiator fans in UT60-280 rad
The PCBs are made by Phanteks and you can connect up to eleven (11) 3 pin fans when using a PWM header. For variable voltage headers. For the variable voltage headers you will be limited to about 2/3 of the header voltage (typically 1 amp) for 1500 rpm fans, 3/4 for 1200 rpm fans. My fans are 0.14 amps and they never go over 850 rpm.
I also have a fan controller (Reeven Six Eyes but only use it to display water temps in and out of each rad and case and ambient air temps.
The Asus FanXpert2 software is very advanced. You can run a system test and it will test all the fans it finds in your system and plot the low and hi rpm points as well as the min start up speed. Then you just look at the fan curve it plotted for you and adjust as you see fit. It does this for the CPU and CHA headers but no.t the OPT headers.
If ya MoBo didn't come with anything like this, ya can always try Speedfan.