If you add the codes to Configurator then they are locked into that Configurator under that profile (not a bad idea to backup the profile if you go this path), you will then not be able to add them the JSS for later use. You would then use Configurator to install and update the apps.
If you use them through the JSS you would them assign them to users and not devices. These are users that have joss accounts and have registered their AppleIDs with your JSS. Once assigned to a user, that user would then have to log into the Apple Store on the iPad and install the app themselves and manage all updates.
How you do it will be determined on how you are managing your devices and if they are shared or single user.
