Your P55M-UD2 motherboard has 1 system fan header with 4 pins. Normally the 4th pin is used for pulse width modulation (PWM) to control the fan speed, like it does with your CPU fan header.
Your manual shows the 4th pin on the system fan as "reserved" or not connected, so it doesn't do anything. Plugging your 3 pin case fan onto this header is normal, with pin #4 being exposed. There is a key in both the header and case fan connector so unless forced, will be plugged in correctly. This fan will run at full speed, but as noted on page 56 of your manual, the System Fan RPM speed (pin #3) and the CPU Fan RPM are measured and reported in the BIOS>