You will need to set one as primary (PLACEHOLDER - BY SOME MEANS I'VE NOT SEEN YET) that will supply details to your federation metadata. This has the benefit that changing from old production version to new production version is just a flick of a switch.
To make a change, click the primary button next to the app and save. Changes will be testable with your own domain accounts within a few minutes. Live apps will update in the federation within six hours.
Anything to watch out for?
Rules are turned on or off on the connection, so if your old and new apps need competing contradictory rules, you my prefer to set up test the new application with its own connection before switching things about.