What's the significance of the E-Book folder?

I’m getting ready to compile my novel to publish as an ebook. I imported all the chapters into the Manuscript folder and then realized there’s an E-Book folder. Does it make any difference if I compile from either folder? Or are they just names for convenience?

Generally speaking, you would use the Manuscript folder for the body of the manuscript itself, and the E-book folder for e-book specific front matter. (Hypothetically, you might be publishing to several different venues, each with different front matter requirements.)

Only documents in the Manuscript folder will be visible to the Compile function’s formatting tools. See Section 24.7.3 for more information about front matter folders.