If you REALLY need the hierarchy, you can number the branches. Or, you can have a keyword for the logical argument with each element a sub-branch of that branch. Otherwise, why worry about it so much? You can link a subject to multiple branches, too. That's one of the beauties of it. You can establish links that the people taking linear notes may not even see.
As far as color, you could always apply color after the class as you're going over the MM. That would give you the opportunity to determine how best to use the color to show the relationships you're seeing.
