Hello Chris - it has to be, surely? !!! If it is, I've been following your OCN thread.
If you want to control both (well, all 4) pumps together, so they all run at the same speed, then you can just use a PWM splitter on channel 4. If you then want RPM reports from more than just one pump you'll have to connect them up to the other headers accordingly, so to monitor all 4 pumps you'll use up a whole aquaero worth of headers, but you'll only need the one PWM header to control them all. I do believe people have sometimes had problems splitting PWM to a lot of fans on a rad or similar, since at some point the signal will be too weak to be split again, but for 4 devices I would expect you to be OK, I guess you'll just have to try it.
If you want separate PWM control of each MCP35x2, then you'll need 2 aquaeros, as there's only one PWM output possible. You could try using a voltage to PWM converter on one of the 3-pin headers, but I haven't tried this and don't know enough about it to recommend any particular solution.
the signal of the second pump to the third channel. Make sure to use the ground on the aquaero to avoid problems with the electronic.
Shoggy, I am about to connect up an MCP35x2 to my aquaero too, and I want to monitor the RPM of both pumps.
Can I just check I've understood correctly - are you saying that for the pump that is connected to, say channel 3, I must connect both the yellow RPM wire and the black ground wire??? The potential of the ground to the aquaero and to the pump are exactly the same anyway, since the pump and aquaero will be connected to the same MOLEX splitter, but if you say it must be connected then of course that is what I'll do.