Using private (i.e. "not shared") is probably best.
Note that shared vs. private simply changes where the config files are stored on the user's machine. In private mode they'll be stored within the user's profile folder (as part of the roaming profile, if you are using one). In shared mode the config will be stored somewhere visible to all users on the machine.
(Note that shared mode doesn't do anything across machines unless you manually redirect the config folder to a network path.)
So if you want different config for different users, private mode is the way to go, definitely. Although if you only ever have one user logged on to any machine at a time then you could use shared mode if you really wanted to (by changing the logon scripts to overwrite the shared config).
Whatever you do, you can automate things by simply copying the config files to the appropriate places. There's no need to manually run the Backup & Restore wizard for each user (though if we're talking about a handful of users then that might still make sense). Info about the configuration file locations is here and here.