The most efficient way of doing this would be with Actionscript. First you want to download GreenSock's TweenLite class and get that set up in your AS folder: http://blog.greensock.com/tweenliteas3/

After you've gotten that, it's just a matter of keeping track of which 'window' is currently open (so you can 'close' it) and which one you want to open, and then trigger the alpha-out and alpha-in events when a nav option is clicked.

How familiar are you with Actionscript 3? I can help you along the way if you're not very adept.