Questions about templates in Frame 12

I'm working on a book which will become an ebook.

I chose as my starting spot the "User Guide" and am having trouble getting the Cover, Legal, Contacts, TOC and Index modified, so I imported my entire document into a copy of the Chapter file. I did not begin with an emty file because there is no place for the text to start; instead I clicked "Show Sample" and then deleted the files contents on the body page.

I am unable to modify the object properties of the main flow on the master pages to remove room for side heads. Or rather, I can remove the side heads on the master page but when I move back to the body pages, the file does not update. I am not asked if I want to apply/not apply the master page formats.

Thanks in advance.