There are several ways to upgrade Lotus Notes …. this can be done automatically via Windows MS installers on Boot…. Automatically via Smartupgrade (built into Domino) or manual processes etc. This will deal with the application the users are using.
The Mail Template will not be upgraded unless you choose to. This can be dome again in several way but if you are doing a whole directory then the CONVERT tool will assist you with this. Check out the help for more information.
Now for certain Domino 8 or 8.5 new features to work you need to change the ODS (on disk structure) of the DB’s to allow the changes. Domino 8.0.x ODS 48 Domino 8.5 ODS 51
You need to added the following Notes.ini settings to the server to allow the ODS to be upgraded etc.
Then run a COMPACT -c against the server