Well nowadays one goes up with an instructor to learn the basics and must be certified (or signed out by an instructor) before flying on one’s own–at least in the U.S. The manual is studied on the ground (usually far away from the plane) and written checklists are done on the ground or done as a shared task between multiple pilots.
But I think we have digressed fom discussing a manual for software. Suffice it to say the pilot analogy was not applicable.