Regarding Photos and its file structure, if I want to back up my photographs to an external hard drive, what files do I identify to be copied over? That is, if I back up the Photos Library, am I actually protecting the pictures themselves (or just links to them)?
If you started a new library from scratch - read: did not convert from a previous iPhoto or Aperture library - then the
Your Library Name.photoslibrary bundle contains everything.
Exception: If you are using a referenced library (Photos menu > Preferences > General > Importing: "Copy files" box is not checked) then you need to back up the folder(s) where your actual photos are located as well.
If you did convert from a previous library, and have not removed it, you should back up both to be safe (though theoretically backing up just one should back up everything).