@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!
Another fan of Fusion Pro Desktop here. This is exactly what you need. We have sold both PrintShop Mail and Fusion Pro Desktop for this very application (numbering) and other VDP applications. Fusion Pro Desktop easily beats PrintShop Mail from both a price and performance viewpoint. You could also try Printer's Bench http://www.elkriversystems.com/ProductsList.aspx for a good entry level package

If you’re producing any kind of numbered items in-house that are multiple-up on a sheet where you need to control all the variables to meet your production needs, the autonumbering feature through numbered lists is the way to go! Just step and repeat away & InDesign will do all the work. No need to fool with a seperate “numbers” file or deal with a data merged document. I think it’s by far the best option for basic numbering.
This feature is easiest to use when you combine it with Word's built-in heading styles. However, you can map a custom heading style to the multilevel numbering feature—it just takes more work. Word handles nine levels, but any document with more than four levels should receive a serious developmental edit. More than four becomes confusing and perhaps worse, unreadable.

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
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