Hmmmm...
It seems that Poggle is caught between the two viewpoints Dooku wishes to give out. On the one hand we have the Neimoidians, surely believing Dooku's stance as the Separatist leader, (the irony of Nute Gunray being manipulated by Sidious again), and on the other Jango Fett, fully aware of what is really going on, (fundamental to the Republic's army and then slinking off to be by the side of this army's perceived foe - Dooku and the Separatists).
I believe this because it makes the most sense and nothing is said to contradict it or muddy the waters. Fett is a true mercenary, indifferent to the grand power struggles going on, and so will play his part. The greedy Trade Federation have a genuine greivance with the Republic and are all too keen to join a Separatist movement against it, together with the Commerce Guilds and Banking Clans.
But some confusion is created as I see it by Dooku's words to Poggle. Either Poggle is aware, like Fett, as to what really is going on, but then we have the problem of the "my Master will never allow the Republic to get away with such treachery" line; or he's like the Trade Federation and feels he's contributing to a genuine revolt aginst the Republic by Dooku, in which case why does Dooku weaken himself and talk about returning to his Master in front of Poggle?; something, I'm sure he wouldn't do in front of Gunray.
There's something about that little war-room scene shortly after the attack of the clones that jars with me.