Heir to the Empire, chapter 4, paperback page 55:
Pellaeon licked his lips. "But then . . ."
"Who is it we've brought aboard the Chimaera?" Thrawn finished the question for him. "I should have thought that obvious. Joruus C'baoth--note the telltale mispronunciation of the name Jorus--is a clone."
Pellaeon stared at him. "A clone?"
"Certainly," Thrawn said. "Created from a tissue sample, probably sometime just before the real C'baoth's death."
"Early in the war, in other words," Pellaeon said, swallowing hard. The early clones--or at least those the fleet had faced--had been highly unstable, both mentally and emotionally. "And you deliberately brought this thing aboard my ship?" he demanded.
The Last Command, chapter 11, paperback page 179:
Mara took a deep breath. The very existence of the place had been a sacred trust, known only to a handful of people--the Emperor had made that clear time and time again. But for Thrawn to have a renewable army of clones to throw against the galaxy . . . "I think I know where Thrawn's Spaarti cylinders are."
Even with her rudimentary sensing abilities she could feel the wave of shock that rippled outward from Organa Solo. "Where?" she asked, her voice tightly controlled.
"The Emperor had a private storehouse," Mara said, the words coming out with difficulty. His wizened face seemed to hover before her, those yellow eyes gazing at her in silent and bitter accusation. "It was beneath a mountain on a world he called Wayland--I don't know if it even had an official name. It was where he kept all his private momentos and souvenirs and odd bits of technology he thought might be useful someday. One of the artificial caverns held a complete cloning facility he'd apparently appropriated from one of the clonemasters."
Emphasis added by me to highlight the important parts. Pellaeon was once an officer of the Old Republic fleet, and the clones were an enemy created by unknown "clonemasters" who unleashed them on the galaxy. Add that to the way the clones are feared for their instability and that everyone is shocked and disturbed that Thrawn would resort to using human duplicates in his war effort, implying that the existing stormtroopers are certainly not clones, and the picture you get is completely inconsistent with the prequels.
But I don't mind that; in fact I'm glad of it, because the prequels are lame, and Zahn's idea was much better. And like skyjedi2005 said in another thread, Lucas rebooted the franchise without telling anyone. So the Thrawn trilogy only fits with the original films, which are the only ones that matter anyway.