envy14tpe :
I'm not sure how you use your computer...light gaming or what not, but if you do stress the system then you need good cooling. I use 2fans that are 600--2000rpm and another that is 1000-1450rpm. When gaming I need these fans running at 80% otherwise I prefer them at 30% for normal computer use. The ASRock AXTU software, like SpeedFan, can control the voltage sent to the fans. It's annoying having to adjust fan speeds before and after gaming but it keeps my CPU and GPU under 65C so I'm happy to do so.
So here is what I ended up with...
I downloaded Easy Tune 6 from Gigabyte and discovered that I could in fact control a system fan, only one, but it was the one that I would most like to control. The interface of Easy Tune 6 sucks, so I moved back to Speedfan to try some ideas out. I started studying Speedfan really close and googled everything I could think of. I found in the Configure>Advanced>Chip:IT8728F at $A30 on ISA tab, settings for PWM 1 mode, PWM 2 mode, and PWM 3 mode. By playing around with these, I discovered that I could, in fact, control my CPU fan and Rear case fan, but not the front, side, or top fans. The rear case fan is the most important to control for me, since it has max rpm of 1200. The other case fans all max at 700. By the way, the 3 700 rpm fans move 110 cfm each and the 1200 rpm fan moves around 60. This totals around 220 cfm going in and 170 going out. I think that is adequate for my 4.3 Ghz overclock and 7950 GPU overclocked to 1100 Mhz. Anyways, I'm getting sidetracked, the key was putting PWM 1 mode to ON/OFF, PWM 2 mode to Software controlled, and PWM 3 mode to Software controlled. Then in the Configure>Fan Control tab, I checked the box for Advanced fan control and then made profiles for the Rear fan, CPU fan, and GPU fan. I linked the Rear fan to Pwm2 and the Temp to what I believe is the CPU Die (it seems to show temps slightly lower than my core temps under load) and I linked the CPU fan to Pwm3 and the Temp to all 4 cores with the Method on MAX of speeds. Finally I linked the GPU fan to it's respective pwm and temp, which is much more straightforward. After tweaking the curves a bit and renaming sensors, etc. I have it working in an acceptable manner. Hopefully google will find this and there will finally be a post out here to give someone confidence that this is possible, because I was one step away from just giving up on it.
Thanks envy14tpe and John Bauer. I appreciate your help in solving this, even if it was not direct help, it did lead me in the right direction.