Serial 2 connects right to the pixhawk. You need to enable it by setting the desired baud rate and protocol in the arducopter parameter settings. It works perfectly fine for me.
The usb port on the accessory bay connects to the IMX companion computer. In order to talk to the IMX I installed pymata and use some python code to talk over the usb port with an Arduino.
Thanks for all your all's help.
fpvsteve,
When you activated your serial 2 port, did you just use Mission Planner or Tower? Also, are you using the latest firmware version 1.5.3 or were you able to accomplish this with earlier versions?
-Zack