In the film there will only be one Doughnut ship, and he will be on the bridge of it most of the time. He will also be in the conference room, where he talks to the queen about the Republic needing to start over and such. He’s sort of going to be playing the Tarkin role to the Nemoidians Vader? If that makes any sense.
I’m not certain if I want Dooku to know about Maul, though. I sort of want the Separatists and the Sith to be separate entities. I think it would be cool if the first time we see Maul it’s him attacking Qui Gon. I’m not sure.
Dooku is gonna bail at the start of the final battle, though. He’s going to do what Tarkin didn’t and evacuate.
JEDIT: Thanks for the kind words!
Clones aren’t gonna be a part of my trilogy at all because I can’t think of a way to make Obi Wan serving Bail make sense without that being a separate event. “Clone” Armor will be present in the trilogy, it’s just that it will be precursor Stormtrooper armor.