Y'know, I agree with Morphic.
I think that the easiest way would be to figure out the categories and then divide the disciplines into them.
Off hand, these are the divisions I can come up with:
Before the fall: This would contain things like Scarlet Baruvia or Cthonic Serpent, disciplines that never made it to the temple. This is where we could include information about the temple itself, Reshar and the other nine masters. This is also where the two new Vestiges can be found.
After the fall: This would have things like Bloodstained Gutter or Wyrm's Might. Relatively newer disciplines. This is where we could talk about how the world was affected by the dissemination of martial knowledge.
Initiators In the Outer Planes: Relatively self explanatory. This is where the planar disciplines would be located. We could also include things like outsiders with martial maneuvers. Also we could, in theory, include little tidbits like what happened to the Nine masters' souls after death.
Epic initiators: This is where the epic disciplines would go, as well as other information about epic martial initiators.
Of course, other types or number of divisions are also possible. Such as having a sort of "core" book and more specific things in their own sourcebooks.