If they didnīt clone all the stromtroopers, the Emperor developed a great cloning technology. Remember his clone boied, and the Spaarti cilinders he used to grow clones very quickly, as seen in the Thrawn trilogy.
Also is said that he had several cloning facilities in Byss, Wayland...
About the rclones in the army, in EU books, like RPG books, is shown that (during Palpatine reign) the TIE pilots
, army crew members, army officials... are recruited from the no cloned people. I believe that only the stormtroopers were cloned then. And some of the old clones were used in maintenance works, as is said in the visual guide to episode 3.