Hey, I couldnt help but notice that you got a wire crossed somewhere in there - those panels are 200 Watts, not 200 Amps. To get Watts, you multiply Volts times Amps. So a 200 W panel at 12v would be 200/12 = 16.67Amps. (A panel that size that put out 200 Amps would be quite something, as it was likely producing more power than all the sunlight that was hitting it :)
So, some good points have been brought up. First off; about mounting panels. Solar panels need to be as close as 90 degrees to the incoming sunlight as possible to maximize their power. This means that bolting the panels in place in a flat orientation is not ideal. You will get more production from the same panels if they can be set to different angles, depending on the season and even time of day (or the direction that you park the truck). This makes me think that it maybe makes more sense to try and design a system around panels that are small and light enough that you can pull them out of the back of the truck and set them up on some sort of rack. Did you watch the movie "The Martian"? The panels will come with quick connectors, so they are not that hard to just plug together. You could even lean them up on a rail, with the bottom resting on the ground.
Also, about heat - I am not sure about longevity, but higher temps also reduce efficiency, so a little airflow under the panel is better than mounting them flat to a solid surface. I would skip the flexible stuff - its likely going to be more work than it is worth.
A heavy duty alternator is a great idea if you are going to go with a 12v system (there are advantages to other voltages, but 12v is a good place to start, and should be fine up to about 1000 watts of panels). Forget the wind mill. You will get much higher efficiency with an alternator driven from the engine, and it will be a lot less work to
boot.
The charge controller only handles the
solar power loads, so it would be completely separate from any other charging source. If you wanted to run a generator, you would need a battery charger that took the 120v AC from the generator and made it into the proper voltage to charge your batteries. An alternator has an internal voltage regulator, but it is only designed for lead-acid battery charging - but if you are on a budget, this is likely what you will have anyway. So, the alternator would basically turn your trucks engine into a generator (albeit not a very fuel efficient one).
With solar panels power is never wasted. The controller is basically monitoring the battery, and then feeding as much power to them as they want. Once the batteries are full, it thottles back how much power it applies. The solar panels only produce as much power as the controller requests. Buying a larger size just means that you can expand in the future, and also that you are less likely to overheat it if you run it full-bore all day in the blazing heat. A thing you will discover is that load-shifting is a good way to get more bang for your buck. If there are projects that require more electricity, you do them on sunnier days. If it is cloudy you lay low, or run down all your battery tools, and wait for a good time to charge them. You will note that they are rated in Amps. The reason for this is that current (amps) is what generates heat in wires. Any wire has a certain resistance, and the more amps you push the more "friction" this resistance causes. Remembering that Watts are Volts times Amps, we see that if we double the voltage, we halve the amps for a given array size in watts. You can always add more systems in parallel, or use bigger wires, but sometimes stepping up in voltage is the easier way to go. Again, it depends on how big you want to go.
Really though, 600 watts of panels in a sunny climate will produce quite a lot of power. If you figure 5 hours of good sun, that is 3000wh of energy. A single 18v 5ah battery holds 90 wh, so you could charge around 30 of those batteries (this does not account for losses, but will get you in the ballpark).