There are many ideas floating around of who really was Sifo-Dyas and who really ordered the clones. This is what I think of the situation.

Dooku is still part of the Jedi Order, but he is under the recruit of Darth Sidious. One of Dooku's Jedi Master friends, Sifo-Dyas, sees that the Sith are coming back after the death of Maul. He goes and orders a clone army from the Kaminoans. Darth Sideous learns of this and moves to secure the army for his own purposes. For Dooku's final test he is told to kill Sifo-Dyas so that no one will find out about the clone army for quite some time. After he kills him Dooku goes and deletes all references of Kamino fom the Jedi Archives. Dooku, remembering his battle with the Mandalorians the last Mandalorian, Jango Fett, he goes and recruits him immediately as the prime clone for the army. Sideous now tells the Kaminoans a list of orders that are to be imprinted in the clones, including Order 66. He then announces that he is leaving the Jedi Order and he is the latest joiner of the "Lost Twenty". Sideous decides to orchestrate a major war so that the Jedi will reduce in numbers and so that the clones will be another way for him to exterminate the Jedi.