If you prefer the web editor, know that each time the master branch is committed, the book is generated. While we are in draft, it is recommended to use a separate branch to do the writing. This prevents too many commits in the github repo master, as each time you save your work in the editor, a commit is done. If you use the desktop client, this is far less a problem, because you only synchronize when you made some more changes.
As far as I know, a reference can only be made to something written down in an article, i.e. a separate file. Therefore, it is a good habit to focus on exactly one thing you want to explain/write about in every file.
If you want to refer to another article, that can be done by using a relative path. Like I have done with this link to Getting started with gitbook. It is probably a good habit to check that the links work, by checking the book as it is generated.