The barrel selector is usually used to choose between two different chokes that you might have in each barrel. For example you might have a full choke on the top barrel and a modified on the bottom. In Sporting Clays if the target you are shooting at is really close you want to shoot with a more open choke, such as the modified. If the target is far away the full would be your option.
Another reason to switch barrel order is if you use different types of shells, 7.5 on the top and 8 on the bottom. If the target you are shooting at is showing a belly you would go w/ the 8.
It's up to the shooter but having too many options sometimes can be counter productive. That's why world champions such as George Digweed use Full/Full for his barrel chokes.