Factory manuals are written for the professional mechanic. It is assumed that anyone using a factory manual already has a basic knowledge of mechanics. There are some things in a factory manual that are taken for granted that some backyard mechanics may not know.
Aftermarket manuals like Clymer manuals explain things in layman's terms and may be easier to understand for an untrained mechanic. Although, they do not go into near as much detail as a factory manual. A good example of this is a gearbox. A Clymer manual will show you an exploded view of your gearbox and may even give out some specs or sizes of related shims and bearings. A factory manual will give you all of the specs and sizes (Thickness, diameter, etc.) of each shim and washer and bearing. These measurements are very important when you have a gearbox scattered all over your workbench and don't know what shim goes where. :ohmy:
Like Patman said, if you take the time to look at the exploded views and read the manual, most people can figure it out even if you are not a professional mechanic.
Factory is the way to go IMO. :cool: