Pins to use? For Leonardo with L298N Module for motors, patch already in use

Alright so we have an arduino Leonardo hooked up to a Sensor Shield which is in turn supposed to connect with a L298N for motor control. I'm trying to find out what pins to use on the sensor shield to connect to IN1-IN4 and if there are any code changes that need to be made.

We used this as the primary instructions for setting things up

But we also used Michael Margolis patched version of the AFMotor library to get around the problem AFMotor has with the Leonardo. His code is available here.

That said, ... how do we get this thing running? We've had one engine spin once under circumstances we havn't replicated yet, but otherwise haven't gotten anything to go. Is there code needed beyond updating the library? Also [u]what pins do we need to use[/u] for the connection to the L298N ? I assume the switch of PWM arrangments means it can't be the same as the c98 kit arrangement