1. What are the flat grey disks (donuts) used for?
I believe they are fatigue markers for the AoT version of the game.
2. Are the forces to be evenly distibuted (i.e. should I apply the red banners to half of the figures, and yellow banners to the other half?)?
The forces are scenario specific for both games. You add the banners as the scenario requires. There aren't enough figs to build two equal armies and satisfy the scenario unit requirements. In fact, there's not enough figs in the base game to play all of the AoT scenarios.
Note that there are enough figs to play the C&C version if you use the updated scenarios posted by Richard Borg:
Samurai Battles C&C Scenario Updates