You can do it by either. Obviously I would say that using a PC is the best way because it is faster and you can really get some work done. You can get the same results by hand because its just a cleaner. Its not going to take out swirls or anything like that.
Layering AIO is kind of redundant. Its a cleaner so anything it puts down as far as protection is just going to be removed with the second coat. I don't really think of it as layering. I think of it as going over the car twice with a cleaner. There are no layers where AIO is concerned. SG is what you layer because it won't strip itself off.