I have a similar setup with water cooling and the main system running at 24V. With that, I'd recommend you to follow DC42's advice and feed the 12V power into the fan voltage selector pin. That and maybe just get all of the fans in 12V.
On my system I also went for a separate 12V PSU since with the pump, LEDs, all of the fans and a webcam I'm drawing above 3A total and it made little sense to get a boost converter at this point. As I've mentioned the currents - a word of warning. I don't know how much your water cooling pump is drawing, but if it's as hungry as mine, I would consider hooking it up directly to the 12V converter. In my case I was afraid of overloading the fan selector connector - I think those simple pin connectors aren't rated for more than 1.5-2 amps of continuous power.