If I understand your question correctly, this is how I would work:

1. Create a Color Scheme in your first master: Slide Master Tab > Colors > Customize Colors > Name (e.g. 'Nov06') + adjust colors > Save

2. Create a Font Scheme in your first master: Slide Master Tab > Fonts > Customize Fonts > Name (e.g. 'Nov06') + adjust fonts > Save

3. To make your second master: copy the first: right-click > Duplicate Slide Master

Whenever you want to change colors (or fonts) of the masters, don't change those in the Home Tab but go to the first master en select Slide Master Tab > Colors (or Fonts) > find your 'Nov06' Scheme > right-click > Edit > change colors (or fonts).

In order to have the same changes made to the second master, go to that master and just re-select for both colors and fonts your 'Nov06' schemes. This will update your schemes without having to adjust the color list and font list a second time.