So the extension is the management component, its an all or nothing upgrade for that part. Make sure you backup all your policies before upgrade, if you need to downgrade it will uninstall all your policies so best to grab a copy of those xml files now!
The installer when you upgrade will prompt you for what branch to check into, I would say eval if its new and testing, if you select current it will prompt you that there is an existing version in this branch and ask you if you want to move it to the previous branch or to overwrite it. So to answer your question, you can either do it now, or during the check in. The installers tend not to make much difference with branches, the branches are most useful when you are putting in hotfixes and patches.
I would also say that when you upgrade FRP from 4.3 to 5.0 you will need to get your systems upgraded pretty quickly, I had issues with users unable to access secured network shares until they were updated as an early warning, I only had 10 installs of this so made my life easier.
Thank for your reply!