Two of the pins on your 3-pin fans are voltage and ground. They provide the power to run the fans - the voltage is varied to control the speed. The 3rd pin is a tach or rotation pulse that goes from the fan to the MB to report speed. The 4th pin (if your ever have a 4pin fan) is for PWM or pulse width modulation which can control the speed more accurately by controlling the duration of the voltage pulse which will 'kick' the fan faster or let it slow a little between pulses. Both styles will work fine.
You can plug the 3pin into a 4pin MB plug by aligning the guides on the plug with the 4pin guide. It will only go on one way.