@Aaron: I am stuck exactly with the same problem. I am constructing a style guide document, and thus my content is mainly images, not text. Still I do need numbered chapters in multiple levels, but the automatic numbering seems to be almost impossible as my headings are in separate text boxes. I have tried linking heading text areas, section markers, numbered lists and whatnot, but I am about to revert back to manual numbering instead of battling with this and wasting time! It’s just so devastating, I believe that machines should do what they do best, instead of people keeping track of numbering chapters!
When you're working on a document such as a magazine or a book with many pages in it, using the master page feature in Adobe InDesign CC 2015 to insert automatic page numbering simplifies working with the document. On a master page, you designate the position, font, and size of the page numbers and any additional text you want to accompany the numbers such as the magazine name, date or the word "Page." Then that information appears on every page of the document along with the correct page number. As you work, you can add and remove pages or rearrange entire sections, and the numbers remain accurate.
Almost everything I learned about Word's numbering I learned from the Word newsgroups (especially the Microsoft Word Numbering newsgroup) and from the MS Word MVP FAQ site. The contributions of John McGhie (especially his article about Word's Numbering Explained on the MS Word MVP FAQ site) and Dave Rado are significant. The current page represents a mere summary and application of some of that work.

In the Adobe InDesign document I’m working on here we actually have two master pages, an ‘A’ master and a ‘B’ master so I’m going to select both the left and right hand page frames with the special character in on my ‘A’ master and go to Edit>Copy. I’m then going to double click on my ‘B’ master page and go to Edit>Paste in place. this will then copy the special character and position it in exactly the same place as it appears on my ‘A’ master. numbering in publisher