I start with the open in the bottom and the tighter choke in the top. However, if I get to a station in sporting clays where I am only changing the open choke for one even tighter than the top barrel, it doesn't really matter.
SUPPOSEDLY, the bottom barrel is more in line for recoil and with the mass of the heavier barrel on top flips upward less. Whether there is any truth to that or if one can even tell, I couldn't tell you.
I do know that the high-end fixed choke pigeon guns all have the more open of the two chokes in the bottom barrel