In your manual, page 34 says the fan systems are accessed in BIOS through the M.I.T system menu. On page 42 it describes the settings for the three System Fans.
First, make sure your 3-pin fan connectors are plugged into the 4-pin mobo headers correctly. There is a slot on the connector side, and a tongue rising from the header, that must align. When connected this way, the fans normally will run at full speed all the time. That is the default mode of backwards compatibility for 3-pin fans connected to 4-pin headers - there is no speed control, but the fans DO work and the mobo monitoring system CAN read each fan's actual speed. I suspect that this should work if the ports' options are set to "Normal", and possibly even at any of the settings. IF there is a "Ignore" or "Disabled" setting, do NOT use that.