I do now a way to only see one box, but it is a little bit moving the problem. Some protocols (e.g. Jabber) support offline message storage (on the server). Because of that, you can send messages to it without the need of being online. It is moving the problem, because the next time you come online with the new account, you get all the messages again.
Another (not very nice) way to work around this is writing a plugin. AFAIK, a plugin can generate messages that don't need to leave the system.
Maybe there are other possibilities where I didn't think about yet.
You can also use another program to send notifications to yourself. For example, KOrn is able to accept messages through dcop and set a notification in the system tray (of course, you can also view your message).