This can get confusing, all right. There is a distinction between the fan control STRATEGY, often called the Fan Profile, and the METHOD of controlling the fan speed, often called the Mode of operation of the fan header.
In BIOS Setup there are several options for configuring each fan header, The Fan Profile (or similar term) usually has options such as Normal (automatic control of speed according to temperture measured by a relevant sensor), Turbo (constant full speed), Quiet (constant slow speed), Manual (you specify a constant setting) or Custom (similar to Normal, but YOU decide what the "curve" of fan speed versus temperature should be). The header MODE relates to the type of signal that is sent out to a fan to accomplish the speed that the Fan Profile setting has decided. Older 3-pin fans can be controlled ONLY by changing the Voltage supplied to it on its Pin #2. The new 4-pin fans work differently and are supplied with a constant full 12 VDC on Pin #2 at all times, BUT also receive a new PWM signal from Pin #4. Inside the fan motor there is a small chip that uses that PWM signal to modify the flow of current from the 12 VDC supply though the motor windings to vary the speed. MANY mobos today use only 4-pin headers, but offer in each header's congifuration options a choice of whether to use the older Voltage Control Mode (aka DC Mode) or the new PWM Mode.
So, set your Fan Prifile to whatever strategy you wish for deciding what speed to run under changing conditions, and then separately set the MODE the header uses for the fan type you have - in your case, DC or Voltage Mode for your 3-pin fans.