My case houses three fans and my mother board has three plugs labeled power fan witch has three prongs then system fan 1 witch has 4 prongs and system fan 2 witch has three prongs but all the fans have three pronged plugs what goes where?
The motherboard fan header with the four prongs, "SYS_FAN_1" I assume is intended for your CPU cooler, and it allows for variable fan speeds through PWM.
The other fans headers only have three prongs, and is intended for all your remaining fans. These fans will run at full speed, assuming you don't have a fan controller - either separate or from the chassis which controls the fan speed through DC voltage.
"SYS_FAN_2" is for your other fan on the CPU cooler, if your cooler uses two fans for example. I imagine that this would run either at the same speed as SYS_FAN_1, or just run as per usual like the other case fans.