The fans you are looking at, Antec Tri-cool Can be run off 4 or 3 pin, but they have a speed control switch(on a short cable) to make them faster or slower.
If you want the board to control them, just plug them into your motherboard and let it deal with them.
Not all boards control fans as well, so depending on your board, you will have different options.
Also note that slowing those fans down with the board may reduce the LED brightness while they are slowed. With the built in switch, the LED's will stay bright no matter the speed setting(L-M-H).
From the look of it, you can run molex and still see the speed with another plug connected to the board.