Whether you use the pump with the signal wire or not, you can control both pumps with the Aquaaero 6.
You will need to switch the output to Power Controlled for the pump with no sensor wire, the other pump you can control with Speed Control or Power control.
I have just fitted a DDC Ultra to my AQ6, all I had to do was cut and solder on a 3pin plug. The speed sensor was on it's own 3 pin plug while the power was off a Molex.