Correct, do NOT use the two ports marked "PWM 1 & 2" for pumps or fans.
And correct, use the four Fan ports for PWM pumps and fans, just select "PWM controlled" under the Advanced section of the aquaero fans tab.
Hopefully you can set your motherboard BIOS to ignore the CPU FAN status. If not, the far right, lower port on the aquero marked "RPM" generates a synthetic RPM that can be connected to the motherboard's CPU fan header to spoof the motherboard.