The BES does not "own" a domain. When you setup a BES, it does not do anything to your mail users, everything will work as before. Only when you create a user on the BES, it will handle that user.
How do the devices know what server to activate against
Each device has service books that get created when you do the Enterprise Acrtivation. The service book contains information, which server the device is connected to (i.e. your BES server ID). So, before you activate, you create the user on the BES. Then, the user activates, which triggers a mail that is sent to his e-mail address. As this address is now handled by the BES, it can pickup the mail and send the correct service books to the device.