Staggering the seam locations will add a small amount to the strength of the construction.

Flipping alternate panels will help to disguise the seams by reducing the ability of the observer to establish any pattern. They would have to rotate the boat to see that alternate panels even had seams.

About the ugliest/worst case would be to cut your panels so that the seam lines almost lined up - but not quite. Then the slightly offset seam lines on adjacent panels would attract undesireable attention.

Now if you could manage to get all the seam lines perfectly aligned, then I'd suggest you treat the area as a trompe l'oeuil joke. Use black paint and draw on a dashed-line "zipper", right on top of the seams. With a metallic brass paint add a zipper pull tab. Next to that add the words, "To shorten boat for storage, unzip here". You can do that in a nice typeface on your computer (on thin paper decoupaged under the epoxy or varnish) and it will look more official.

Hope this helps.

PGJ