There are some foundational set up things that you can do in InDesign that will set up your content for success.
Parent pages (the feature that used to be called master pages) are the place that a typesetter would set up the text fame, running heads, folios, etc. There is often a little more space in the gutter of a print book for thick spine reasons, and along the bottom margin for thumb reasons. The designer may set up columns or layout grids using guides in the parent pages. The main thing for ebook developers to know about parent pages is that this is where you keep things that need to appear in print but function differently for digital, so we want to keep them out of the way. The running heads and folios are generated by the reading system.