You will need the mod BannerPaste to paste the banner.
You will also want Banner Color Persistence by quakunk which will ensure your banner looks correct when loading a game.
Make your banner. Copy it using the button above. Press Ctrl+V in the Banner Editor
You can change your banner by pressing B on the campaign map, or by clicking the banner in the top left of the Clan screen.
For version e1.7.0 or later, there is a newer version of the editor here.