Hi Seevee,
I have solar panels (2 large rigid panels) on the roof of my pilothouse, installed last spring, so I only have experience with them of one summer. I also had solar on my previous boat, a sailboat where I had both rigid and flexible panels (one each).
We installed 2 fairly large panels on the Pilothouse roof of Pilitak (NT37) a year ago. The panels are monocyrstalline, solid aluminum framed with glass tops and are about 280 watts each (if I remember correctly – close anyway).
My suggestions for a solar install:
Put on the largest panels (total output) you can fit! More capacity is better in this case and the price difference in up sizing is not substantial when looking at the whole project.
Use MPPT type of controller, not the PWM type (especially for converting the unused voltage into useable amps). Some suggest using a separate controller for each panel which will maximize battery input when there is partial shading. I only used one Morning Star MPPT controller with a remote panel for “watching what is going on”. Use a quality brand controller (not the place to cut costs). Other good brands include: BlueSky, Outback, Genasun, etc.
Mount them in a location where shading from overhead items will be minimal and unless you are going to automate having the panels “point to the sun”, mount them basically flat, pointing straight up. In the Florida sun (hot), you want good air flow around them (under them as well) for optimal cooling. (As stated above by DW).
I installed mine so as to not penetrate the roof. Worried about future leaks. I attached stainless steel tubing to the existing hand rails above the pilothouse doors, to make a “mounting frame”. I then attached the panels to the tube “frames” using four (4) plastic adjustable “tube mounts”. I did the physical install myself, but did use a marine electrician for the electrical, but it was fairly straight forward for someone with some DIY electrical experience.
Anyway, I am happy with the total install after one season. Any day where the sun was out (not foggy) the solar restored my battery bank back to 100% each day by about 2PM (or earlier). I only ran the generator to make hot water (on a couple of occasions) and when we had heavy fog for a few days! We were out for over 3 months and put about 20 hours on the generator. Most of the time we were at anchor or docks with no power (say 70% of the time). We were out in over 30 knot winds, and did not have any problems with the mounting system.
Some background: we use golf cart 6v batteries totaling about 650 AH and run a fridge/freezer, separate freezer (24/7), electric head, lights, pumps, etc.
My panels are approx. 3 feet by 6 feet each in size. To optimize output, you could use several smaller panels, all with separate controller, but your cost to purchase and install would go way up (compared) and the gain might not be that great (if the available total watts were equal), therefore, cost to benefit may not be there.
Running the generator in the AM to make hotwater, bulk charge the batteries, (and whatever else you may need AC power for) would definitely almost guarantee having a good solar installation getting your batteries back to 100% each day. (I have found that generator running is not needed on most summer days here in western Canada). Your batteries will last longer if brought back to 100% charge (almost) everyday as a side benefit to solar. Without solar (or wind, etc) most boaters who do not "plug in" regularly do not get the batteries back to 100% near often enough for optimal battery life, and are in effect "murdering their batteries".
Hope this helps with your decision,
Tom