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It seems to me, by the way he set things up, that Palpatine always intended for the Republic to win the Clone War. I'm sure he had some contingency plan for if the Jedi lead forces suffered a catastrophic collapse and the separatists won but that would have been "Plan B".
Did Count Dooku know that the separatists were supposed lose, or was he trying to genuinely win the war?
No. "Tarkin" novel (New Disney Canon) by James Luceno indicates that in the conversation Tarkin had with Dooku:
“I am committed to the idea of a galaxy ruled by an enlightened leader, with laws that apply universally—not one set for the Core Worlds, another for the Outer Rim worlds.”
“An autocracy,” Tarkin said. “Guided by the count of Serenno.” {{ DVK's comment - that was Dooku's title}}
Dooku gestured in dismissal. “I am ambitious, but not to that degree.”
“Who, then?” Tarkin pressed.
“We’ll leave that for another day. I’m simply trying to keep you from finding yourself on the losing side.”
As we know from novelization of Episode III, Dooku full well knew that Chanellor Palpatine was the same person as his Sith Master, Darth Sidious. Therefore, the plans for "ambitious" person to guide the Galaxy always were to be Palpatine as far as Dooku was concerned.
This shows in the same dialog later:
The count nodded in assessment. “I may not be able to forestall repercussions, Governor, but should this situation escalate to war between the Confederacy and the Republic, I will do my best to see that no lasting harm comes to your homeworld.”
Tarkin’s brows beetled. “Why would you?”
“Because in the end, you and I are likely to find ourselves under the same roof.”
Please note that the "finding yourself on the losing side" quip is a red herring - further in the Tarkin book it's explained that Dooku merely was testing Tarkin's loyalty for Sidious.
{{Narrator's voice, showing Sidious' internal thought process}} Tarkin had remained loyal during the Clone Wars as well, enlisting in the military on the side of the Republic, despite repeated entreaties by Count Dooku — which Sidious had arranged as a test of Tarkin’s dedication.
In the novelization of Revenge of the Sith, Dooku reflects on the plan for his defeat and capture at Anakin's hands:
Again, Dooku sighed. Today he felt every hour of his eighty-three years. "It is ...fatiguing, to play the villain for so long, Master. I find myself looking forward to an honorable captivity."
A captivity that would allow him to sit out the rest of the war in comfort; a captivity that would allow him to forswear his former allegiances—when he would conveniently appear to finally discover the true extent of the Separatists' crimes against civilization—and bind himself to the new government with his reputation for integrity and idealism fully intact.
The new government...
This had been their star of destiny for lo, these many years.
Revenge of the Sith (novelization), Chapter 2
The section goes on to elaborate on the rest of the plan—Obi-Wan is to be killed, Anakin is to be turned to the Dark Side, and the Republic is to be reformed into the Empire. Dooku is apparently unaware of Sidious's plans for the Jedi Purge, since the plan also calls for the Jedi Order to be converted into a "Sith Army", but otherwise believes the Republic/Empire will remain, and that this has been the plan all along.
