As I regularly fans through the aquaero, I do not want to regulate the fan with aquasuite.
If I am understanding you correctly, you want to control the Aquaero fan headers though the hardware correct?
If so it is a pain, but can be done via the three buttons on the Aquaero. Then you save the settings via an eprom write and you are done. You don't have to use the Aquasuite software.
As gr3if mentioned above, the fast way is to use the Aquasuite
to program the Aquaero and then you don't need it anymore.