Your first post says, "I can control it with the low,mid,hi on the computer case but when I try to control it with programs it dont work.". That tells me that ALL of the fans you that you cannot control are connected to a central hub of some kind - maybe a small circuit board - that is controlled entirely by a push-button on your CASE, and NOT to any mobo fan header. You also listed two fans, but now say there are three - front, top, and rear. Moreover you say BOTH the front and top cool the radiator, which I doubt. Maybe that is not what you meant.
Let's start with the fan that IS on the rad. Is that one fan or two? Trace where its motor power cable goes. For many AIO cooler systems it should go to the CPU_FAN header on the mobo or to CPU_OPT. SOME AIO systems use a different connection, but you have not told us what your CPU cooler system is. The rad fan(s) should be controlled by CPU_FAN or CPU_OPT because those are the headers that WILL control automatically according to the temperature sensor inside the CPU chip.
Now re-trace where the fan(s) for the CASE are plugged in. It / they should go to a CHA_FAN header. I From your description I would guess they go to that circuit board, and NOT to any CHA_FAN header.