question

If connected in series it sounds like the maximum voltage presented to the charge controller is 52.8VDC at 5A for a total of 264W. Since this voltage is under the "100" first number in the model name, you should be safe.

Every cell of a solar panel is in essence a diode. It will only allow current to flow in a single direction. In a typical panel there are strings of cells. In a good-quality panel there are perhaps three bypass diodes within the design. These allow current to flow around problematic substrings (which have reduced current due to the shading).

So if you connect panels in series and one is partially shaded—assuming that there are bypass diodes within the design—then the current just flows through that without adding additional voltage nor drastically reducing the current that was produced in the other two. If your panels include "half-cut cells" then these are more forgiving to shading.

The orientation of the shading is significant. A vertical shade from a mast along an entire column of cells would in many cases knock the output down a lot as opposed to a horizontal shading across the same panel. I'm assuming a "portrait" orientation of the panel here versus "landscape".

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If connected in parallel then you're presenting a relatively low voltage to your charge controller. You haven't mentioned the voltage of your combined batteries. In a 12VDC battery storage system the solar voltage in the 17-18VDC isn't significantly more than the 12V it's trying to charge. If you have a 24VDC battery storage system then you're attempting to charge with a lower voltage and the SmartSolar will have to "change gears" and switch from a more typical stepping-down operation to a stepping-up for voltage. (I recently changed a client's solar system from eight panels in parallel to four panels in series now doubled in parallel [4S-P-4S]. This quadrupled the voltage presented to the charge controller and the entire system then began working wonderfully by comparison to before.)

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I would recommend connecting them in series.

As for the orientation of how they're pointed, I think it would be important to discuss if your boat is moving or not. If this is a sailboat and you're making figure eights between two buoys then you won't show a panel directly to the sun at all times. In a case like this I think I would recommend getting two vertically-mounted bifacial panels along the centerline of the ship.

Thank you very much for the answers.

Indeed we are using 12V system of batteries (two 200Ah batteries in parallel).

Boat is simple Merry Fisher and we use it just for family usage, but why do we need much charging power is because summer trip with kidds. We go about 3-4 weeks island hopping staying in each place about 2-3 day. And this is where we need good solar charging. While we are underway it is no problem because of 150A alternator on engine. So problem is while we are stationary :)

So tu sum up, can this work in paralel with 12v batteries? I dont want to go into percentage of usability, but can this work like this without damage to any of system components (solar panels, mppt charger, batteries)?