I knew the day I decided to replace the old Nautique that this project was coming. We spent all last season dealiwith the old deteriorating, smelly, wet carpet. I ordered 3 long sheets on ebay at the end of summer last year and and had enough to go from driver feet/ observer compartment to the v drive and under the rear bench seat. Did not do anything in the bow, and went a different route under the sun pad.
So on to the floor...first few steps were to remove all the items and stuff in the boat. Pull out and store the cushions. All the seat bases in my boat are removable and screwed down in to the floor on top of the carpet. Pull those to store as well.
I didn't really take any pics up until this point except this one. When I received the foam last year I pulled the 2 removable floor panels and added the foam. I did so because, in my head, it was the majority of the carpet and would go quick.
In my opinion, DO NOT DO THIS. I had to tip-toe around the finished panels while cleaning the glue out.
At this point with the interior out I could measure and estimate where my seams would fall. And I used a straight edge and sharpie to mark where the eva lines on those panels needed to fall on the carpet templates once removed. 6-8" forward of the panels is an access door, carry the lines on to that as well.
Those sharpie lines became vital while templates the carpet. I very very slowly cut the carpet where I believed the seam should be (turns out I was a stipe off but it was easy to fix with the clean cut)
Pull out the carpet.
Goo gone gel worked better than 3m general purpose adhesive remover, and much cheaper.
Use the old carpet as a template, trace and cut. Clean the floor really well, and stick down pieces. Removing the backing on the big pieces was tough, due to size.
Most of my seams and edges are not visible. Hidden in the back of the compartments, or under seat bases. The ones that are in visible areas i carefully lined up the stripes and stuck it down.
Where the foam folds down between panels, I added some stainless staples.
For ease of service I added a pull handle on the front corner of the removable floor, no prying on the new foam...
Re install interior. Clean carpet before they go back in.
I added vents to the seatbases as well to hopefully cut down on some moisture. 
For the vdrive compartments, I did not like the thought of buying more foam to sit, wet, under ballast bags. I park on a bit of a hill and always end up with water sitting in those compartments. I pulled the carpet, cleaned the glue, removed about an inch of the vertical carpet around the bottom of the compartment to hopefully keep it dry. I hit the raw floor and walls with black rattle can paint and placed in these rubber drain through mats. They piece together and give maybe a quarter inch gap under it. 
We are very happy how it all turned out.
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