No one knew full extent of Sidious's plans, but Dooku was most privy
Dooku was Palpatine's apprentice and second of Two Sith. He certainly knew about true role of Clone Army, including Order 66. He actually participated in creation of said army. He also knew that CIS rebellion was just a tool, and that Droid Army would be shut down when is no longer needed. Being a bit of idealist, Dooku dreamed of humanocentric empire (which did happen, sort of), ruled by Sith and those Jedi that joined them. He envisioned Anakin as an enforcer in this empire, which also did happen. Only thing he did not know was that his master Palpatine never cared about anything except himself, and that he never intended to share power with Dooku.
Mas Amedda is an interesting character, always near Palpatine, but for someone so close to most important events in Galaxy, very few things about himself are known, and even less about what he knew. He was of course aware that Palpatine had great Force powers, maybe even that he is a Sith, but so far there is no proof that Amedda knew about Sith Grand Plan or Order 66.
As for Jar Jar Binks, he is just failed comic relief. If Lucas had any different plans with him, that was all cancelled because audience hated him so much.