I put them in the top since it's redundant steel with the floor .... kind of like the factory rails only had three sides to make most efficient use of the floor. Actually the only reason I did this at all was because my factory rails were trashed as it's not the most efficient way to add stiffness to the chassis.
Regardless I'm not sure I agree with you for all load cases in this application. You are correct that the more the metal is from the center the stiffer the beam will be ... high moment of inertia .... however, I'm more worried by the yield case if you were to bottom out on a sharp object, jack in the wrong place, etc since the section is relatively thin vs the potential normal force that could be placed on it. I wanted to minimize the chance of screwing up (off road, slipped jackstand, etc) and kinking the beam. 1" tall tube is not much then start adding holes and well if you look up at my cracked factory frame rail pic and you can see where I'm coming from. This is the reason I went with 0.083 vs .065 wall was to prevent a jack or jackstand or curb from denting them otherwise this thick stuff is just dead weight. I just wish my factory rails weren't beat up so I didn't even have to mess with this ... and they didn't even have spec of rust on them.
Cameron