The controller is a solid-state electronic box that controls the power (speed) between the batteries and the motor.
My controller is a Curtis 400 amp peak PWM controller designed for use with series-wound motors. It can run on 48-72 volts.
The higher amperage your controller is, the better your acceleration will be. The higher voltage, the better top speed and efficiency of the car.
Also, keep in mind that amperage is also what defines range in a battery. Capacity is marked in Amp Hours, but draining a battery at double the amps will give you LESS than half the run time! Having a controller running higher voltage will use LESS amps to do the same amount of work.
What's this mean? Buy the highest voltage controller you can afford! 48 volt controllers are cheap, as they are used in so many golf carts. 100V+ controllers get expensive real fast.
My 72V controller seemed to be a good compromise of cost and efficiency. I bought it slightly used on E-Bay for $300.
Follow the schematics available through the controller manufacturer to connect the batteries to the controller and motor with heavy gauge cabling, such as welding cable, with solid, heavy-duty lug terminals on the end.
The controller requires a 0-5Kohm potentiometer as a "throttle". This could be as simple as a $3 Radio Shack part, or as fancy as a purchased, specialty part such as a Curtis PB-6
I split the difference and installed a 0-5K pot inside a free-from-the-junkyard forklift throttle control.
Run the gas pedal cable to the potentiometer, so that when your foot is on the gas, it sends a variable signal to the controller.
Update! I later switched over to running an Open ReVolt motor controller. It's the same one you can find here on Instructables at http://www.instructables.com/id/Homemade-100-HP-Motor-Controller-for-an-Electric-C/
That controller is good for up to 144V and 500amps.