I am debating using the case fan controller for the three case fans initially and then tacking any extras onto the motherboard.
I do things a little outside the box. The CPU fan is of course plugged into the motherboard. My case fans are always being run from 7VDC, to which I make my own power adapters from a 4 pin molex to 3 pin fan header. Yellow (+12VDC) which goes to the (+) fan wire, and red (+5VDC) which goes to the (-) fan wire. The voltage difference is 7VDC. I've not met a power supply that could not handle it. This provides enough voltage to start the fans running and keeps them running at a slow speed. I get constant airflow across my drives and through the case.
As for the fan placement for the D5 case, depending on your removable drive bays, if they are well vented, I'd use at least one more fan to exhaust air, thus causing air to be pulled in across the removable drives. 2 front fans (intake), one rear fan (exhaust), two top rear fans (exhaust). I would not blow air down on top of the removable drives as the top unit
might get the benefit but the lower unit definitely would not.
You could buy a pack of smoke sticks to help see how the air is flowing for example. Or use toilet paper and place a piece across the front of the removable drivee bays. If it sticks well then job well done. If it does not stick then fix the airflow problem.
I hope this makes sense.