File>>Save will save the current document. So, in a VI window, it will save the VI. In a project window, it saves the project.
Project>>Save Project will save the project associated with the current document. So, in a VI window, it will save the project (if the VI is opened from one). In a project window, it (obviously) saves the project.
The shortcut menus is the same as the File menu
Save.
Save All (this Project) saves all open files in the current open project.
Christina Rogers
Principal Product Owner, LabVIEW R&D