@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!
It sure is possible! Numbering and Section options are available in the Pages Panel menu. These options allow you to define what page starts a section and how it should be numbered. Insert a Current Page Number marker (Type>Insert Special Character>Markers>Current Page Number) in a text frame on a page or master page (recommended), select the first page of your section, open the Numbering and Section Options dialog, and enter 200 in the Start Page Numbering at: field. Hope this helps!

Changing the numbering display affects how pages are indicated in the InDesign document, as in the Pages panel and in the page box at the bottom of a document window. The numbering display also affects how you specify page ranges when printing and exporting the document. However, the numbering display does not change the appearance of page numbers on document pages. numbering in indesign