There is no "step by step" manual. There are a couple of books out, including Audio Editing With Cool Edit Pro by Robert Riley. I see copies every so often (since there's no longer a Cool Edit Pro, I guess they haven't bothered to reprint it). I have one, and it was useful, but you will always find yourself wanting to do something that the writer didn't think of. The best way is to start at the beginning and teach yourself.
One thing I have found with the books is that all of them assume you understand recording, music, and arranging, and that all you need is to know how to configure your ins & outs, sampling rates, etc. If you don't know what ins & outs ARE, or why sampling rates matter (or that they exist) then a book won't help. CEP (and most of the other software I've seen) emulate tape recording for a lot of their functions, which means sometimes that if you can't use a tape deck it's not going to be any easier to use a computer.
A lot of people sort of assume that, if it's a computer, it will do a lot of things for you, kind of like a graphics program that "automatically" gets rid of red-eye in portraits. The truth is, that recording is a deep and complex activity, and, while a computer will do many things that you either can't do without one, or without a lot of expensive analog gear, it's still a box. It won't take my voice and guitar and turn it into Hoyt Axton Sings With Steely Dan, but it WILL allow me to get the combination to sound as good as possible.
All that said, here's a link to a CEP manual:
http://www.alfors.com/Ruzne/cep2man.pdf
