OK, so obviously, as someone state previously, Dooku is just feigning ignorance in front of the Separatist leaders. He is well aware of the clone army's existence, after all, he had a hand in having it created. So, my conclusions are:

1. It was Sidious who ordered the clone army built, using the alias of the dead Jedi, Cypha Dias(I know I spelled it wrong). He ordered it done by his apprentice, Dooku.

2. It was Sidious who incited the separatist movement so that the crisis would reach a fever pitch and the Senate would grant him supreme emergency powers.

Now, my questions are:

A. If the Jedi had not found out about Jango Fett and the clone army, would Palpatine have used this army against the separatists as a ploy to trick the Republic anyway? Palpatine says that he will build a grand army of the Republic. Was he planning to unveil the clones all along or did he now have to go along since the Jedi had discovered their existence?

B. Was it Palpatine who erased the Jedi archives' records of the planet Kamino, or does Sidious have another accomplice inside the Jedi order? Yoda said only a Jedi could have erased the files.

Originally posted by Exar Kun II
A. If the Jedi had not found out about Jango Fett and the clone army, would Palpatine have used this army against the separatists as a ploy to trick the Republic anyway? Palpatine says that he will build a grand army of the Republic. Was he planning to unveil the clones all along or did he now have to go along since the Jedi had discovered their existence?
Well I have my own theory on this, since palpatine is the emporer, he has forseen all this. So he knows how its going to play out, and what the final outcome will be.

Dooku had to have erased the files, before he left the Jedi Order.

Originally posted by Redwing
Dooku had to have erased the files, before he left the Jedi Order.

Perhaps, however, if the order was placed 10 years prior, Dooku would not have been Sidious' understudy, it would still have been Darth Maul. How long ago did Dooku leave the order?

or

Perhaps Dooku was a Dark Jedi, and when Maul was killed, Sidious elevated Dooku to full Sith apprenticeship.

it doesn't seem like dooku is a apprentice, he seems more like a follower.

Palpatine was trying to kill Padme Amidala, being the leader of the opposition against the law to create a Republic army. So ask yourself: what would have happened if he had succeeded at killing her? Political tumults, maybe.

Possible, that there would have been no such law, because people would have been so shocked and thus voted for her cause as an act of post-mortem support. So what would have happened then?

Anyone dressed as a Jedi could have walked to these Kaminoan fools and taken over the army. Maybe they could even have taken the army for the separatist movement, Sidious revealing himself and then attacking the Republic, allying up with the Seperatists? Well, that may be a little far off...

On the other hand, maybe he would have gotten supreme emergency powers anyway, because everyone would have said: "look at these seperatists! They are terrorists! We need to do something about it!! Create an army!"

(Waidaminute... does anyone see parallels to a current head of a super power, today, in a galaxy very very very close to us? War against terrorism? Helloooooo. No way that Lucas was aiming at George "John Wayne" Bush, though... ;) )

uhhh...where was I? Oh yeah.
Also: Palpatine could have secretly given the Jedi a hint to ensure that they find out. He knows the Jedi are clever. He even ordered the Jedi to protect Padme. THis way he could make sure that after a second attack, they would do everything to find the identity of the attacker.

He planned it all well, that bastard...

it doesn't seem like dooku is a apprentice, he seems more like a follower.Well, of course Dooku is the apprentice. Not as in "the young unexperienced Jedi Padawan apprentice" but in the Sith there are only two, no more, no less. One Master and one Apprentice. This way it was set up by Darth Bane who re-established the Sith Cult after the Sith kept destroying each other to get more power.
Sidious is obiously the master, so Dooku has to be the apprentice. The only other possibility would be that he is no Sith at all but only a dark Jedi. That again is impossible, he is clearly a Sith as you can see from how he treats Sidious ("my master" and so on.)