Others have already advised - lower barrel is on the lower axis of the gun / recoils directly into your shoulder / in theory less abusive to gun - and less muzzle rise, but muzzle rise is only an issue is you have a 2nd shot to take ( on doubles, or Continental Trap where you can shoot a 2nd shell ).
I prefer an O/U vs a single barrel Trap gun ( like the Browning BT-100 ) - but its the weight, feel, swing characteristics of the O/U that makes it the gun I prefer - and it means I can shoot 1 Trap gun ( for any of the Trap games / singles, doubles, continental ).
I always load the lower barrel on an O/U for a single shot - matter of a consistent pre-shot routine and I leave the barrel selector so the bottom barrel is always the barrel that fires first. I don't switch the barrel selector around / and I stay with the routine of only loading the bottom barrel / partly so I don't screw up and load the Top barrel - and go click - and lose a Target... A lost Target in Trap - is a big loss - since 100 straights are commonplace in competition.
A good solid pre-shot routine is important if you're striving for consistency on your scores. In my case...
1. after I shoot my bird, open the gun, remove spent shell ..
2. head down - focus on ground - or close and rest my eyes - and I don't watch as the next 2 shooters call and shoot.
3. after I hear the 2nd shooters gun go off / I look up - focus my eyes on my hold point - and keeping my gun open, I drop a new shell in lowe barrel chamber(but don't close the gun) - (Its allowed under PITA rules).
4. I watch the 3rd bird / and the 4th shooters bird - for any effect from the wind ( see if it slides, drops, or hovers ...).
5. I close my gun / mount my gun / go to my hold point / Focus / think "nose of target" - Call - and fire...... ( and do it 24 more times ...)
Whatever your routine is / stay with it - and switching the barrel selector back and forth would be a mistake. By the same token - if you want to shoot the upper barrel on an O/U there isn't really any reason not to either - and on a good gun, both barrels will have a Point Of Impact that is the same.
On a gun with a ported barrel - you will notice the lower barrel has more holes in it typically than the upper barrel / to help reduce the muzzle flip - so we fire the bottom barrel first / to keep muzzle flip to a minimum - so we can see the target for the 2nd shell better.