[The_Victor]

I saw the Discovery Channel show on Ballard's mapping/excavation of the Black sea wreck. But the wrecks always seem to have the jars in a jumble or maybe an aligned pile. I don't think I've seen anything about how they were placed in the hull of the boats.

Anyway, it's just one of those nagging questions that Discovery Channel never seems to answer.

[SunkenCiv]

See my answer above — the grain or straw would be long gone, leaving the jars in a jumble.

[TigersEye]

What amazes me about Roman amphoras is how big some of them are. 80 gallons or better. Yet the handles seem relatively small. The pottery must be stronger than I imagine to support that weight without the handles snapping off.