Working in iOS I've never dealt with OS X and NSDocument based apps. Where should the model reference live, inside the NSDocument or the representedObject in the NSWindow's content NSViewController? Or both?
It should be stored in the NSDocument object as stated by the Apple documentation in here. In particular, check Figure 1-1. Further below, on the same page, Apple states that a data model corresponds to a document type, so if you have different models you should use different document types that should be stored in NSDocument objects.