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Did Dooku know that Senator Palpatine was Darth Sidious? This is a dumb question, I know, but Dooku looked confused when Palpatine ordered Anakin to kill him. So was Dooku a pawn in the whole thing?

Yes he knew, he looked confused because Palpatine promised him clemency once the war was over

In EP 2 he tells Obiwan about the trade federation betrayal to Obiwan. Dooku says thousands of senators are controlled by the dark lord, at this point it seems obvious that Sidious is Palpatine

He knew Dooku was weaker then Skywalker. He wanted Dooku dead so he has a younger and more powerful apprientice, Skywalker. He knew he needed more power to rule the galaxy once more.

Of course he knew. As a matter of fact Dooku and Sidious had a discussion about Obi and Anakin several minutes before they arrived. Grievous is the idiot..he had no idea. In the novel there were more lines to the holo conversation. Grievous asked Sidious why he hadn't been allowed to kill the Chancellor.