[John Lessnau]

Ok, I figured out what to do. When filtering message to labels, there is also a check box to also move to archive, this archives the message out of the inbox and moves the message to the label. Problem solved.

Now my next problem is that I really don't like the built in email app as compared to Snappermail. Snappermail seemed to have many more features. I'll give the built in app a bit of a chance before a make any changes though.