As far as replacing the existing file, on the floppy, you have three optons:
1. Save your backup to a different floppy. 2. Save you backup with a different name on the existing floppy. (if there is enough room on the disk) 3. Replace the data from the previous backup on the floppy.
If you replace the existing file and the new backup has some errors you may not use the previous backup to restore the project.
As far as saving the project and library files separately, this is only necessary if you have more that one project. You can save the library files and then save each of your projects associated with those library files.
With 3.0, if you save your projects with separate library files then this does not apply and you must save each project with separate libries as a complete backup.
Saving the library file only once does not apply to the next backup cycle only to the backups being performed at the same time.