The question was to keep the emails from going to the messages box. You cannot. The message box is the folder they go into, and when you setup your email on your BB you add a shortcut to those email addys. Messages will go to both.
You can seperate SMS/MMS however, but this will not affect emails. you will just get another folder for SMS/MMS and they will not be in the messages folder.
You will still have the messages folder for all emails whether or not you have the SMS seperate.