I shoot bottom, my son shoots top. I've had a few guys tell me o/u's are designed to shoot bottom first. They say o/u's are designed for doubles trap. Saying the bottom shoots a little high for the first shot, and the top barrel shoots straighter. Meaning shoot the first clay on the way up and the second as it peaks.
Others say the recoil of the lower barrel is less as it is more in line with your shoulder etc, making it easier to line up that second shot from the top barrel. Having said all that, barrel convergence varies, and gun fit varies. Shoot what you want, and what works for you.