You can use any other two PWM pins to control the second motor and
connect these PWM pins to connector J3 on the Rugged Motor Driver
shield (pins EN1 and EN2). Then, use any free digital I/O pins to set
the stepper motor direction (pins DIR1 and DIR2). Since the motor
driver already uses PWM pins D3 and D11 you may choose from D5, D6,
D9, and D10 for the two additional PWM pins.
You can then stack one motor driver on the Arduino then stack the LCD
shield on top of that, and keep the second motor driver separate, or
just keep both motor drivers separate (i.e., not stacked) to allow for
better heat dissipation.
This extra wiring can be done using soldering of wires, or you can use
something like our Quick Shield to sit in between the Arduino and the
first board you stack, then just connect wires from that. On the motor
driver, you can solder directly to the EN1/EN2/DIR1/DIR2 pins or get
the 6-pin connector from our motor driver upgrade kit and do it all
without soldering.
Hope that helps.