Open the Message application, go to options -> general options. There is an option in there called "SMS and Email Inboxes". That will let you separate them. I think that is what you want to know.
Does anyone know how to set the default folder for messages? I'm trying to get it to default to Inbox instead of every type of message.
There should be a folder that is just listed as "messages", everything comes through this on my Tour (all email address, bbm, yahoo im, facebook, etc). Try placing a shortcut on your homepage for this folder and move all of the other mail folders to a lower location so they wont show up on the homescreen.