You will need the mod Banner Color Persistence by quakunk which will allow you to paste your banner and 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 versions of the game prior to e1.7.0, there is an older version of the editor here.