Hi Justin. You could replace just the section in the main salon and the head area, but several things argue against it. First, you may not be able to find matching teak and holly plywood. The OEM installation on my boat had more of a reddish cherry look to it and the replacement wood is much browner. Second, while you can probaly remove sections cleanly I found it desirable to change the seam in the salon, which ran through the bilge access openings to a location more under the salon table. Third, a good part of the time required is from setting up the work area, so once you are set up it takes relatively less time to cut additional sections. So the bottom line is, you might as well dive in rather than wade in from the shallow end.
As for how to install the two layers (the 1/2" ply between the stringers and the 1/4" finish floor) since the underlayment has to be attached to the stringers (which Ericson did with screws and silicone) you really cannot glue the underlayment to the top layer and then install everything. Ericson installed the underlayer and then glued the top layer to the underlayer. My plan is to do the same, but screw the top layer to the underlayer, but I haven't worked out the details yet. I would like to find some sort of bedding compound that has no adhesion (to allow removal) to give the top layer a more solid feel and even out any minor imperfections in the underlayer. Failing that, I will try the non-slip mesh I mentioned earlier.