So here's the deal. If you use Plugins, you'll have to wait for a new version of the FreeNAS PBI to become available in the Plugins browser (the part that shows the list of available apps). Plugins are designed to be point and click, but we're still working out the process to automate the build of PBIs as newer versions become available.
If you create your own jails using Jails, you have much more flexibility, but you also need to have more knowledge. It's a good idea to skim through the whole Jails chapter first to see what functionality is available and to decide which type of jail and which type of software installation method best meets your needs. This chapter currently describes all available software installation methods. I've made a mental note to add how to upgrade currently installed apps.