The update script executes the new scripts on the files in the database on the host specified in servers.php. The Update All option has worked fine for a long time, it'd be interesting to see the actual error you get. A "duplicate column error" could mean anything.
It's been a very long time since i've used the manual sql credential method to walmartone update anything, i'll see if there's anything that can be done to make it more efficient.