Channels equal "real" separations. Layers are a way of sort of pseudo separations. Channels have tremendous flexibility where not just separations, but also art creation is concerned. Channels are how Photoshop does separations. When you set up your separations in channels, you can go to the print dialog and set halftones, screen angles, registration and trim marks, etc., on a "per color" basis. You can view all of your channels in color, with transparency, and print black and white, since channels are grayscale. They just are viewed in color. Press print once and get all of your films in one go, just like Illustrator. If you're using layers, then you might be doing things like making a layer black, pressing print, come back, turn off a layer, turn another on, make black, press print, come back, and do that over and over til you get all of your film. Some people do similar stuff in Illustrator and it's not necessary in either. Not even when you have underbases or various other specialized screens. You can still press print once and get all of your film from the printer. So the upside is, this is actually how separations are done. I don't know if there's a downside since this is how Photoshop is meant to function. I would advise you to begin learning channels. There are a lot of tricks and great interaction between layers and channels both when creating art and doing separations. Layers and channels have their own special features which are not possible in the other.
