The scorpion looks like it is designed strictly for Rc use, so It needs a Servo type control, Not PWM and direction.
Bad News, pwm and Direction won't work.
Good news, you can use the Serialzers Servo command to control the scorpion.
Bad news, all the PID stuff (Mogo, Digo) is tied to PWm and Dir so it won't work with the servo command.
You can use the servo command and so your own PID on the higher processor, at least that will tell you if the encoders are working properly. The Encoders are NOPT tied to pwm in any way so they will still work fine.
Ringo
If you low pass filter(resistor and capacitor) the PWM you get an analog voltage. Unfortunately what you get is 0-5V for a pwm of 0 to 100. What the controllers you mentioned want is 2.5V for no movement, then close to 5V is forward, close to 0 is reverse. You could use these H-bridges and the serializers PWM command, but again MOGO and DIGO would not work. I did some searching briefly and did not find anything that works below 12V. Try posting on Comp.robotics.Misc or some of the big club sites (PARTS, Seattle robotics, etc) and see if anybody has a recommendation. Higher Amps at a lower voltage, I don't know if anybody has anything like that.
One alternative is to use 12V, and limit the speed in your software to a max of 7.2/12 of the maximum speed, then your motors would be seeing essentially 7.2V at max.