The ECU is mounted behind the battery. You're referring to the relay box. The arrangement is identical to my '07. I just removed the mounting bracket/hardware, and zip-tied all the sub-harnesses together. It sits in the pocket near (but higher than) the stock location. Never had any problems.
If memory serves, I think I moved the routing up over the front intake duct so it wasn't so dangly. I can PM you pics if needed.