I think having the CD on top, like you have it would definitely help. There is a lot of air space in the top of the empeg, but the mainboard (and temp sensor) is pretty much right against the bottom of the empeg. If it does get too hot, I pull the empeg and put in on the seat. The CD player is so hot that if I reach inside the empeg sled, I can't hold my hand on the bottom of the sled. I know, I know, how can I possibly put my poor empeg through this abuse? I have an upgrade planned to fix this in the near future.
Warranty is voided on my truck empeg already, so it is not an issue. Also, if I do attach the fan, I think I would drill the sled and attach it to the outside of the sled and run it off the ACC line.