If you open an Xcode 4.x project at Xcode 5 and then open a xib at Interface Builder, you will get an alert:
In the File Inspector for the xib (cmd-opt-1), you can change the "Opens in" popup to say "Xcode 4.6". This will revert the document format to one that is compatible with Xcode 4.6, but it also means you will not be able to take advantage of some of the new capabilities in Xcode with regards to xibs.
If you want to "reset" the "Always upgrade" choice you made, you can do that by resetting that particular user default using Terminal:
defaults write com.apple.dt.xcode IBAlwaysUpgradeAutolayoutDocuments -bool false