Hi Anutami,
Personally, I'd suggest that you go with Option #1.... Simply scootch the panels as far as possible to the left (& eliminate the gap between the panels) and move the cargo box all the way to the right. When possible you might choose park facing east (preferred, as this should cause no shadowing), north, or south... then crack open a cold beer and stop worrying about batteries and charging.
Based on the amount of shadowing you get, you will likely want to go with parallel wiring so that you can achieve some charging when the shadows get long (because your photos were shot in mid-day sun, I don't have a good feel for how severe the shadowing will be). Also, you didn't mention the spec's of the panels, how you plan to wire them (series or parallel), and what brand/model of charge controller you will be using. If you provide that info, you may get a different range of solutions that what you have received so far.
I assume you have a plan for some type of ladder so you can access the cargo box?
Cheers
-Mark