I have shot alot of trap over the years and dont currently shoot with a o/u. However it was always the 'RULE" that the bottom barrel was the best as it gave a more direct bore to shoulder alignment and resulted in less felt recoil. A trapshooter can easily shoot 300 rounds a day so any advantage no matter how slight is a bonus.
Bottom barrel, because of reduced eccentricity, if screw-in chokes. If fixed chokes, select the barrel with the choke appropriate for the distance you're shooting.
Real Trap guns have only one barrel (because trap shooters get confused by two).
For those of us less fortunate that don't have a shotgun for every game....
I shoot a Beretta sporting clays gun for trap and always use the bottom barrel as the slight upward angle of the lower barrel helps to compensate for the lower rib on the barrel compared to the high rib on a dedicated trap gun. I do very well at the trap range with my "compromised" gun.
Good luck
E.