Here is video from several years ago but I think it a good example of how a hatchery works when stocking musky.  The Minor E. Clark Hatchery in Morehead, Kentucky stocks several species of fish through out the state of Kentucky and it was a build when Cave Run Lake was impounded in 1969.  The reason for this was it allowed them to have a running freshwater access site to help raise the fish.  This video goes through how they collect the muskies from the river and lake, the spawning of the fish and how they are raised and recaptured in the ponds.  Musky stocking is key to fisheries across the country and this will give you a glimpse of how this process takes place.