How is your system currently wired, knowing that would help me understand where your problems are. I've got a similar setup to you expect my Modem is different. I have a personally purchased Modem and from it, is the Airport Extreme. From there I have the Netgear (XHS) router plugged in to it. There are no ports or changes you need to make on the AEBS (Airport Extreme). I have some Gigabit switches in here as well but they are all just Pass-through as my back bone.
What does work?
What doesn't work? (Can't connect to the Internet, Can't connect to the panel via Internet)