Now that I'm a member proper I wanted to post a more comprehensive reply on this, for the benefit of those who may not yet have started on hull thickening. Firstly let me correct the sizes I gave above - in fact I used 3mm, 2mm & 1mm respectively, approx. metric measurements as evergreen comes in imperial. I'm attaching some photos here to illustrate what I have to say.
One photo shows how I thickened the port side, by 'boxing in' around each gun port. I copied this idea from somewhere though that builder probably did it much more tidily. My thinking was that it wouldn't show from the outside so the scruffiness wouldn't matter. I'll come back to that presently. After creating the boxes around each port I then lined the inside of each one with 0.5mm evergreen, cutting strips from a sheet and leaving it long on the inside, trimming off the excess later; there's a photo of this. I tried to cut the liners as accurately as possible, to avoid filling and filing later, and set the liners depth in the port by eye. This whole process was, to be honest, very, very tedious. In some ways it led to me parking the project for 5 or 6 years, because by the end of it I'd realised there was a better way, thought I ought to start all over again and re-do the port side, but couldn't face it. I even bought a second kit cheaply on ebay a few months later but still couldn't find the motivation! (I started again in January this year, why is another story for another day, but in any case with a strategy - this should be pleasure, not torture, so I stop when I'm getting bored and only pick up again when I'm in the mood. If it takes me another 10 years to complete it, fine.)
Another photo shows how I 'strip thickened' the starboard hull. In this instance I set the long evergreen strips on the two lower decks perpendicular to the horizontal rather than flat against the hull, so the sills and lintels would be true to real life, otherwise it'll look weird and there'll be hardly any space for the guns to poke through. I haven't worried about that on the upper deck as, at 1mm thickness, it doesn't really have that effect and a little filing before lining sorts out the top. I then (obviously) added the short verticals either side but didn't worry about precision as any gaps here are very easy to fill later. For the liners, this time I used 0.5mm evergreen of three different widths, 4mm, 3.2mm and 2.mm respectively, setting the back edge in line with the back of the thickener and tweaking once all four pieces of the liner are in place and the glue is still wet. I also didn't try so hard to cut the liners accurately, close enough is good enough, and have used vallejo filler to seal the corners and joints. This has been a much, much better method than that I used for the port side. It still takes a lot of time, I'd guess 10 or 20 hours including filing off the poorly moulded liners and tidying up, but the end result looks more like it's part of the ship than boxing in. Incidentally, I've found that vallejo is the best filler for that particular job as it has a very fine nozzle and you can run the filler into the corners quite nicely. It is also very easy to scrape and chisel rather than file off the excess, giving sharper lines.
To return to the scruffy port side. Having dry fitted I can see that the boxes on the upper deck will be visible so I'll need to tidy these up and make them look the same as the starboard side. To me at least the starboard side looks great through the deck, the port side dreadful.
I suspect other builders would have known this beginners error from the outset, and I'd point you to foxy's build on this site (7732-hms-victory-by-foxy-heller) as an example of a really tidy piece of work. Of course I only discovered that last night! Note though what I said in my original post about wide evergreen fouling the line of some holes.