Within Master Roadmapping you also have the ability to Color By Field to highlight your dataset. By selecting the Colors tab you can see all the available fields.
Another great way to compare Items across roadmaps is by selecting a common Field for your Header under the Layout tab then in the Colors tab Color By Source. This provides you the ability to see how Items in different Source roadmaps align with one another.
When creating a new Palette, you will have full control to choose how you would like to color each Header, Item and Milestone.