What I do is connect to the #4 fan header but powered from the psu....I only monitor rpm's from one pump but pwm signal from both pumps. Never really saw a need to monitor rpm from both pumps (MCP35x2).
That is also the way I had it connected ............... however , I read in some thread that some connect in this way ( monitoring both RPM's ) and wanted to know if there is any real benefit that I'dont know in this way.