Getting a Backbone--
I'm working right now on what will be essentially a getting started workbook. It will probably consists of an interactive document that queries the user for configuration-specific information, such as network topology, operating modes, etc., and it will provide specific user assistance for the user's configuration requirements. The latter might be delivered in discrete deployment guides (probably delivered as conventional PDFs) while the interactive document would be used primarily to determine which guide to point the user to.
So the core of the workbook is NOT procedural information, that comes later. The core must be conceptual information and guidance information so that the user can make informed decisions about how to configure the product. The flow of the topics will be determined by the deployment process, with the most important information being conceptual (background about the product) and guidance (considerations, criteria, and consequences of decisions that the user must make). After that, the user can be directed to detailed procedural information.
I've had a tendency in the past to view procedural information as the backbone of a user assistance document. The old P-K analysis approach: Define what procedures the user must do, then analyze what other kinds of knowledge you must impart for them to understand the procedures. I'm certainly not throwing that baby away with the bath, but I'm coming to see less and less importance in defining the sequence of steps and seeing more importance in imparting expertise to support the user's application-level goals.
In short, if it's that hard to figure out how to work the application, shoot the UI developer. The challenge for the UA should be helping the user figure out how to apply the application to the user's goals.
Make the higher order information (what I've been calling conceptual and guidance) the backbone of the user assistance, and let procedural information branch off and out from that core.