Hi Spineman,
There is no set answer to your question, if you are a new builder then Id suggest going along with the build instructions.
You will learn shortcuts and better solutions as you build and remember these for your next build.
To answer some points of your question though, applying decking before any consecutive upper decking is obviously necessary. Applying the decking before false keel, if this means laying the deck planks before you even install the false deck to the ribs then I wouldn't do this - the deck generally has to follow a curve from bow to stern (and sometimes port to starboard) adding decking first will make the false deck too thick to follow the shape of the false keel and be difficult to nail / clamp in place.

Ive not heard of any problems in this area with the SF build so I'm guessing its a pretty standard method of construction, good luck

Steve