What I do is pick a color, then stick with the same color hexadecimal number for both my custom banner AND for editing my save game so then they both match up.
Earlier, I would create a custom banner with one color and then try to match it up when I'm editing my save game. The result is close, but much more of a guessing game.
So this way, I just use any online site like the one below to choose a color, find out its hexadecimal enumeration and then just stick with it for BOTH my custom banner color AND my Editing my save game, so they both agree.
Any color picker site like this works wonders:
http://www.colorpicker.com/