I like to try and hide that inside joint behind or near a rib for visual cleanliness but it really doesn't matter as far as strength goes as long as the scarf is a solid joint.
A properly fitted and glued scarf joint will be stronger than the parent wood you join. If you make a sample joint on some scrap plywood and bust it the wood adjacent to the scarf will yield, not the glued joint.
I haven't nailed through a glued joint but a drilled pilot hole might make it easier to get the nail through and into the framing assuming its a hardwood. I'd think the scarf's location it would be determined by trying to best utilize the plywood. Just my humble opinion, eh.
I've done both. No difference. The only thing i try to avoid is putting a scarf on a hard curve, as it will show as a flat spot. I know the boat you are building and you have no hard bends. Put it where it falls!