streetsports :
Deuce65...I'm doing it this way because I would rather fan expert control them than the corsair link...and from what I've been reading they interfere with each other if you try using both.
Oh. Well wouldn't it be easier (and cheaper) to just buy anything BUT a corsair kit if you don't like the software? They're all made by asatek anyways....But anyways for your question yea as long as you connect the pump power connection to power and the 3 pin to CPU fan header it will be fine. You can do whatever you want with the fans.
Do NOT connect the fans to CPU fan header, that needs to be the pump. The point of attaching the pump the the CPU fan header is to feed the RPM signal to the MB. That way if your pump dies, it will read 0 RPM and PC won't start ((or will shut down if it is already running). If you don't connect it, the PC won't know the pump is dead and won't care until it shuts down from overheating.