I learned to sep the old fashioned way, but have had different sep programs over the years as they definitely speed up the process. If you want to learn to do that, Mitch Different's offering on separating is quite good. As others mention, the files usually need tweaking, though not bad out of the box. It takes experience to learn to see what's going on at the press to be able to decide how you might tweak your separations. I use UltraSeps here, as it really speeds things up. I also know my way around Photoshop, which doesn't hurt at all. You get and learn to use the tools so you can go ahead and work and get the job done, time will just make you better at it.
Steve