RacAtat007 :
Are the fans powered through a fan header on the motherboard or plugged directly in to power? I'm guessing they are all through the Mobo in which case you should be able to use the bios to control them. Have you checked your temps after the install because it may be either the temp is reading wrong and your pc thinks it's overheating or your actually running hot and the fans are running full speed. In afterburner you have to select manual mode at the bottom after setting the fan speeds.
My back 140mm fan is plugged into a splitter on the other side of the motherboard, and my 2 cpu cooler fans are connected to the motherboard. One is in cpu_fan1, and the other is in cpu_fan2. exactly like my stock fans were, before I switched them out for 2x Corsair fans. I have tried bios, but it doesn't do anything. When I save settings and boot my pc, and open a game for about 2 minutes, they start to spin fast. I tried opening afterburner, and when I clicked it, it immediately started to go crazy. Tried to shut the process down from the task manager, and they're still really fast. I have to reboot to make them quiet again.
Edit: My temperatures (in celcius) are: GPU at 28c idle, CPU at 27c idle. They go to about 30-35, sometimes 40 depending on the game, when I play. If I understands this correctly, these temps are more than fine.