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Hereby is used in connection with what is present with the speaker or what the speaker has just mentioned or the speaker's present words (i.e. the present document); thereby is used in connection with what is at a distance from the speaker or what has been mentioned by the speaker or by someone else.
In terms of when to use them, \include is commonly used to put each chapter of a book or thesis into its own file. I keep a set of shortcut commands that I use in almost all of my documents in a .tex file in my path, and then \input it in the preamble of any document that needs to use them.