Although you can upgrade ATV Flash via the settings under Maintenance this is not possible for an iOS upgrade. To upgrade iOS you need to redo the jailbreak.
Before attempting to do so you probably want to use the Backup options under the Maintenance menu to save all your current settings. Then after doing a new jailbreak and re-installing ATV Flash you can then use the complementary restore option to get back your current settings.
Note: I believe that there can be issues re-installing ATV Flash (as the installer always tries to install the latest version) if you do not currently have support for ATV Flash active so this is something to check. I believe others have managed to resolve this by contacting FireCore support.
I cannot find the Maintenance Menu in ATVFlash to upgrade the ATVFlash software. Where is this located? (I just updated nitoTV to 0.8.4 and I am still not sure what version of ATVFlash I have; where do I find this again?)
My Menus are: Movies, TV Shows, nitoTV, Music, XBMC, Internet, Browser, Computers, Media and Settings
License just expired, so do i have to pay another $29 to get the ATV flash SW? I have 2.2.2 ATV flash installed on ATV, but now want to update my ATV to 5.x., which looks like i need the latest SW on my MAC, which i did not download.