What the manual describes does NOT answer OP's problem. It does indicate that you have some choices available, but does not explain what those are. There are "modes" to choose, plus a Customized option. It is common to have "modes" include Automatic (a pre-set group of parameters for automatic control based on temperature measurements), Manual (you set a speed and it stays there), Max Cool (full speed at all times) and Quiet Mode (reduced fan speeds as much as possible to reduce fan noise). But none of these are detailed in the manual, so we don't know from that what really is available. The manual also does NOT say anything about whether the 4-pin mobo port can be set instead to operate as a 3-pin port, which is really what OP needs to use his 3-pin fans.
IF those fan ports are always going to work as 4-pin ports, it does not matter what speed mode you select. ALL of them will be implemented by changing the output of the port in 4-pin mode. What does that mean?
Well, a 4-pin fan port has 4 signals. Pin #1 is Ground, Pin #2 is the +12VDC power supply, Pin #3 carries the speed pulse signal generated inside the fan motor back to the mobo for monitoring, and Pin #4 carries the PWM signal. Inside the fan motor is a small chip uses the PWM signal to modify when current from the +12VDC line actually flows through the motor. It is this last signal, PWM, that changes to alter fan speed.
On a 3-pin fan the first three pins are similar with one important difference. Pin #2 is still the +VDC supply, but this is the signal that is varied to change the motor speed. It is not always +12VDC. That is why, when you plug one of these fans into a 4-pin port where Pin #2 is ALWAYS +12 VDC the motor always runs at full speed.
So, as I suggested, OP should look at exactly what the BIOS Setup screen for those ports say. IF they offer the option to change the port to 3-pin mode or "Voltaqe Control Mode" that's the right choice, and then the other options can work. Unless that option is there, no other choices in BIOS Setup will change the problem.