I just started using Google Apps for my domain. I have been using your pro version for my standard Gmail account and I love it. I just loaded the Beta Google Apps (Multiple Accounts). So far it seems to work well. However I have a feature missing that is in the Single Account Pro version. It may actually be there but I don't know it.
The system tray icon is the envelope just like always and it has the green outline. When I have new mail in either account (2 accounts setup) it never changes color. I loved that about the standard pro version so if I was away from my desk and came back it was very obvious I had mail (gray outline turns to blue outline)
This may have been mentioned in another thread but I wanted to add this as I really like that feature and I hope it will be implemented (if not already) in the Google Apps (Multiple Accounts) version. Any time frame on a Pro version as I would like to purchase asap. Thank you for the awesome app.