Two ways to do this.
1. If you have BES, you can setup BES to handle one email address, and then setup BWC to handle another. They both come into the Messages application on the handheld, but they have distinct "from" and "reply to" options for outgoing messages. Only real restriction is that "reply" will always use the same email address the message was sent to. However, there is no way to segregate the messages INSIDE the Messages application on the handhled. In order to do that, you need to go to No. 2, below
2. Get a third party email application -- something like EmailViewer from Reqwireless (I think -- I have never really used this one, but it seems to work). Setup the third party application to work with the non Exchange based email address, and have BES handle the Exchange server. You should be able to keep the two applciations completely separate.
Now, of course, I could be wrong