@yono:
One of the most comprehensive and FREE manuals I have come across covering a few different ways to master key the same locks with different bitting (depth) systems was produced by Corbin-Russwin...
<< External link to download file: CR_CylinderManual.pdf >>
It covers the differences between single-step progression keying systems versus two-step progression... How to "divide the key" to create the hierarchy of your master key system... It also explains the mathematics of master keying very well...
Definitely worth reading to refresh yourself on the basics of masterkeying even if you aren't using Corbin-Russwin products... It is FREE -- I have a couple of books on the subject that cost between $40 and $60 each, which get very technical about the subject which might be a little intense for someone unfamiliar with the topic... Yono, I know you aren't a beginner with locks, but it sounds like you haven't created many keying systems from scratch before, let me know if you have any additional questions after checking out the CR Cylinder Manual...
~~ Evan