Hook the pwm/rpm from the MCP35x2 to the Fan 4 header as it's the only one pwm capable, and run the power from your psu, not from the Aquaero and you should be fine. As soon as you get Aquasuite loaded and flash the firmware go to the Fans tab and set the Fan 4 header (pwm connected to the MCP35x2) and set it for PWM control under Advanced settings.
I believe all the power settings default to 100% so your fans will be running wide open until you get everything setup and adjusted the way you want them controlled.

You should probably only have one Aquaero USB connected at a time until you get the firmware flashed as the software tends to get confused at first with two Aquaero's connected via USB.
In other words, go ahead and connect all your fans, pumps etc but only connect USB to one Aquaero at a time until each one is firmware flashed, then you can connect USB to both and be good to go.

As long as the MCP35x2 pumps are connected to power they will run, so you won't get any meltdowns. You may see the fans shut down during firmware flashing but the pumps should run since it's directly connected to psu via the 4 pin molex.
HTH.

For ultimate safety and near idiot-proofing for the initial setup, leave your power configuration however it is currently or just temporarily connect the pumps and a few fans to regular power supply headers or motherboard headers. Connect nothing to the Aquaero, just connect power and USB on one of the units.

Boot up, get everything flashed on that one, then power down and connect the second Aquaero.

Boot up again, flash everything, set up your basic outputs, set everything to 100% power, power down.

Now put your power connectors in their final locations, boot again, and set your curves/final power levels for everything.

Seems convoluted, but it won't take long. As long as the pumps are running, you'll only need maybe one or two fans going. It'd take a while for the system to overheat at idle without fans, the pumps are the critical part.

Yeah, like Jeremy said, you don't want anything connected to the Aquaero when you flash the firmware. I didn't think about this (wasn't really awake) when I replied this morning. But I was also making the point that only the Fan 4 header is pwm controlled so after the firmware is flashed that would be the header to connect the pwm wire from your MCP35x2 pumps.
He laid out the steps to follow pretty well.