In that case, you can use analog inputs ADC6 and ADC7 on the 3pi to read your joystick channel voltages. These two pins are jumpered by default to hardware on the robot, but you can remove these jumpers to use the pins for your own inputs. The Pololu AVR Library makes it easy to read analog voltages on arbitrary analog inputs, so that part should be easy. I suggest you start by just trying to read the voltages from your joystick channels (you can display the readings on the LCD for easy feedback).
After that, you need a function to convert the readings into motor voltages. Assuming you want one joystick channel to control throttle (forward/reverse) and the other to control steering (left/right), you will need to mix the channel readings appropriately to get your motor speeds. Typically, this mixing is something like:
motor 1 speed = scale factor * (joystick ch 1 + joystick ch 2)
motor 2 speed = scale factor * (joystick ch 1 - joystick ch 2)
This assumes that joystick channel 1 is throttle and channel 2 is steering. Note that if the steering channel is zero, both motors are set to the same speed (the throttle channel), and if the throttle channel is zero, both motors are set to opposite speeds (set by the steering channel).
Does this make sense? If you have specific questions, please ask. Otherwise, I think you should just start playing around with it and asking questions as you run into trouble or come across things you don't understand how to do.