Roelof,
Now I understand much better what you meant in your first post.
First of all, you should read a bit about "Projects" in the Help file that comes with the program. Press F1 or Help, and read chapter 25 - Templates and Projects
As they say there: "It helps to think of a project like a folder that gathers all of your shows together into one larger group."
A project doesn't move your files from where they are on your hard disk, it doesn't modify your files in any way, and it does not save them any differently than the regular process of saving the individual shows.
It's just an "organizer" that helps you load all the shows in one place, and on screen at the same time.
It doesn't really matter how you choose to save, as long as you don't forget to do it
The option "Save Project and All Shows" just saves you time. In one click you save everything.
If your shows have been already saved, then you would choose just to save the project.
It is up to you to decide what is better suited for your needs.
But, just as a side note: Pay attention to the asterix (the starlike symbol) placed next to the name of an unsaved show, as opposed to no sign at all next to a show that has been already saved.
This might show you what kind of saving would be best in each case.