The problem is that the menu bar item does not allow you to distinguish between which inbox holds the fresh email, and neither do the icons or text that appear on the Growl alert messages. So, although it says that it it works for multiple accounts, it really only works to aggregate multiple accounts.
If you use Gmail on a Mac, you should consider checking out Notify. It’s a great-looking, compact app that sits in your menubar and tells you when you have new Gmail messages. It works with up to 4 Gmail accounts, and also supports Growl notifications.