I had pretty much the same problem when fitting solar panels to my electric boat. My first attempt was to buy some raw cells so that I could do as you intend, fit the tiling pattern to the shape of the fore and aft decks. I did several experiments and none were very successful, as it is fairly difficult to get good results without using a vacuum system, I found.
I can tell you what doesn't work, which may help.
- laying the cells on glass cloth and encapsulating with clear epoxy, of the sort used for casting, produced a tolerable result at first but the cells cracked from the difference in expansion coefficients (this is important, I found, as the cells will easily reach 50 to 60 deg C in bright sun).
- Laying the cells face down on clear polycarbonate, then encapsulating the rear with Dow Corning two part silicone produced a panel that worked well, was slightly flexible and the cells didn't crack. The downsides were all the air bubbles between the cell faces and polycarbonate and the poor light transmissivity of polycarbonate, which reduced power a fair bit.
- laying cells face down on acrylic sheet (Perspex) and encapsulating with the clear Dow Corning stuff worked the same as the polycarbonate, but gave much better performance. It still looks unsightly, though, with all the air bubbles.
If I were tempted to do this again then I'd opt to use acrylic sheet, the Dow Corning resin and try and rig a way to put it under vacuum to get the air bubbles out. You'd need to maintain the vacuum for several hours, as the resin sets very slowly, and it would help if you had a way to hold the cells face down to the acrylic, as they tend to float up in the resin I found. I was tempted to try embedding a piece of woven glass cloth on the rear, as I believe that might add strength and help protect the rear of the cells better. The Dow Corning resin is expensive, but I don't believe there is anything else that is really usable for DIY use. It remains slightly soft, even when fully cured, and so allows for the differential expansion that's inevitable with the different materials used.
I ended up fitting a canopy to my boat to which I installed four 50 W flexible panels from Sunflex. Not as cheap as DIY. I believe Sunflex may make custom shaped panels, certainly they asked me what shape I wanted mine and where I wanted the terminal box located, so they might be worth contacting. They laminate the cells inside a layer of EVA, with a thin aluminium back plate and a tough plastic top surface (which may be acrylic I believe).