Power all your case fans of your psu with the 4pin molex connectors.
There is absolutely no reason to use mobo fan headers for case fans.
The only fan you need to power off your mobo is the cooler on the cpu-fan header.
I only attach fans to the motherboard that I want to monitor. That is, CPU fan, chipset fan (if I had to add it), HDD-cage fan, the fan-pulse signal from my PSU, etc... Of course, if you can't monitor all those ports, than the point is moot.
I'm not sure why mobo manufacturers started putting extra fan power ports on their boards, but back in the day, if you wanted extra fans, they were powered directly from your supply. Just cause the ports are on the board doesn't mean you have to use them.
Still, it probably doesn't hurt to use them either, so I don't really see any reason not to just do what you want to do.