First off, I have to thank ​ for his help in getting us to our current position.  We see the value in the Skeleton Sketch Part Method because inevitably near the end of our projects we are having to make fundamental design changes.  So, we need a robust method of handling those changes to our assemblies.  I worked with John and tried to map out what I thought would be a good workflow. 

Currently, we are struggling with how we are to set up our "zones" and we are hoping that someone that uses this method for something like ship building can give some additional guidance.  For instance, my current thinking is that machinery attached to the movable span should be part of the movable span (machinery subassembly with SSP should be in the movable span ASM).  My previous thinking was that all of my machinery should be in a "master machinery" assembly.  This is all so new to me that I am having trouble wrapping my head around all of it.  I reached out to our VAR and they offered a one on one 2 day web session.  I don't want to go that route because we have 5 people who will actively be using SolidWorks with this method.  I'll follow-up and see about on-site training for all 5 of us.  In the meantime, I was hoping there was someone out there who uses this SSP method for large assemblies that could assist us.

Here's a little background:

We design movable bridges with civil, mechanical, electrical and architectural.  Previously we would recreate the structure from the 2d structural drawings and add our machinery subassemblies (which is our part of the design).  We would end up with close to 10k parts in various subassemblies:

The flow chart for the next bridge I am working on may be something like this (which is a different bridge type than pictured above):

Notice the "M2 Clutch ASM" is part of the "Tower Machinery ASM" which is part of the "Towers ASM".  This is my current thought process in breaking this down.  This is instead of having the Clutch ASM reside in a "Master Machinery" assembly that would be in the Bridge ASM.

As part of this process we plan to continue to document the procedure (see the attachment),  It already has a simple example for anyone interested in test driving the SSP method.