I read that in days of yore when O/U double guns were becoming popular, people used the bottom barrel because that's how those guns were originally set up - you couldn't decide which barrel to use first, so if you were shooting singles, it had to be the bottom barrel.The bottom barrel mitigates recoil. It is a matter of physics. By using the bottom barrel, the recoil is directed more toward your shoulder and not up into your cheek. In other words, the recoil is located closer to the pivot point.
Welcome to the clays game. You'll be spending more on more on guns and gear as you go further down the rabbit hole. Glad to read that both you and your wife are enjoying it. Maybe we can get a group together to shoot some clays at PG after tax season. Used to get together with Lou45, Mopar, and SNI once in a while to shoot trap.
I've almost exclusively used the top barrel for the last few weeks, but I switched and shot a position with the bottom barrel one day, just to see - I didn't seem to have any issues with it and from what I can tell, it seems both barrels pattern the same.
I'm still consistently in the high teens/low 20s for scoring - I shouldn't complain about missing a few per round, but I know that I have the capability of doing better than that. One Friday evening the missus and I went out and were the only ones on Trap 4 at AGC. I need the most work on positions 1 and 5, so we might try to get out there sometime again where we can put in some focused work on just those two positions.
All in all though, I'm digging this shotgun and shooting clays in general.