I use an h50 also. I use an antec 900 case. In other words my fans all have manual controls. I didn't use corsairs included fan. In my bios I set all of my mobos fan controls to be off. Basically in your setup, it appears you are trying to take use of your mobos ability to control fan speeds. The only fan your mobo will dynamically change in response to cpu temp should be the 4 pin fan. So which ever that is on your setup will be controlled by that.
I honestly do not know how the mobo's speed controls would affect pump speed, hence why I turned it off on my setup. Also most mobo's can control system fan (3 pins), but change them based on system temperature not cpu temp. My question would be whether you are trying to maximize cooling, or acoustic performance, or get a mix. If you are going for cooling performance I would shut off your mobos fan controls (fans will run at max). If you are going for acoustic, the situation gets a bit trickier. If you want a mix, your current setup should work fine if I'm understanding you correctly.