Run the pumps into a graduated cylinder. Pretty easy.
Slowing the motor down does not change the 1 to 1 relationship of the pump heads by any means. They run off the same shaft, and are identical dimensions/tubing.
So you have a 1 gallon graduated cylinder (it's what we have at my work) and you run a tube from each pump head into a cylinder, turn on, and time how long it takes to hit a gallon.
Once you know the flowrate of your pump, you can program an OSC or setup a timer to let it do it's thing for throughout the day
Edit:
And for controlling pump speed I'm planning on using pulse width modulation. It's a very simple way to control the speed of a DC motor. Basically you're cylcling the power on/off to it hundreds of times a second. You setup a duty cycle (amount of time the voltage is on per a cycle) and that controls the speed without drawing more current.
So if you take a 12v 200rpm motor, and you run a 100% duty cycle 12v pwm signal to it, the pump runs at 200rpm
If you take a 12v 200 rpm motor, and you run a 25% duty cycle 12v pwm signal to it, the pump now runs at 50rpm
50% would make it 100rpm, yadda yadda