I have had CFS for 11 years, and Fibro for about 7 years. I agree that there is a lot of conflicting info out there. That's because no one really knows what is going on and the ones that have it figured out better arent' being listened to.
As for the differences: I believe that the research shows that CFS and FMS are different illnesses which have overlapping symptoms. Like if you had the allergies and then got a head cold. (Not the best analogy, but the only one I can think of right now) Anyway, many of the symptoms are the same for allergies and head colds, but they are caused by different things and are in fact very different illnesses.
With CFS, most research shows some sort of infectious process with symptoms like sore throats, low grade fevers, swollen glands, sore spots in mouth and on tongue, rashes, muscle aches and pains, and of course, intense fatigue.
With FMS, most research shows this to be more of a disorder of the musculoskeletal system. It involves soft tissue such as muscles but also the joints. It is more in a class with arthritis and the like. This doesn't mean that a person won't have other symptoms like fatigue. That is also a part of it.
So the way to keep them from being confusing is to remember that for CFS, the primary symptoms are viral-like with intense fatigue. With FMS, the primary symptoms are pain, and yes with some fatigue. Some FMS patients have more fatigue, some less.
Anyway, that is what the researchers have been able to show so far. Who knows? Maybe in the future we will find out that we are all wrong about them both. But I don't think so. I believe they are different diseases which have a propensity for each other. That is why they tend to show up together in patients. What the connection is, I don't know, but we will know someday.
Hope this helps.