Here's how to use multiple copies of After Effects at the same time. First, make sure it isn't running, then navigate to the After Effects program in the Finder.
Control click on the application and select Show Package Contents from the pop-up menu. Navigate into the Contents -> MacOS folder, and then make an alias to the After Effects file in that folder. Place the alias somewhere easy to get to, like your Desktop (and/or drag it into your Dock for quick access). Now you can use this link to open After Effects, and it will open as many times as you click on the link. Note that it will open the Terminal also, and show all the open process.
By this way you can render in one copy of After Effects while working in another one.
[robg adds: I don't have After Effects, so I can't test this one.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060713094900651