Collating an RTL "book" in InDesign CC

I've been working on a siddur, or Jewish prayerbook, in InDesign. However, all of my training has been in the "document", creation within InDesign, which is to say, I can make perfectly decent layouts, but I don't know how to string everything together.

I did attempt to compile a "book" with the files which I already had, however the result was that I lost all of my RTL formatting and needed to completely redo it. How do I compile an RTL "book" in InDesign?