Automated will 'approve' based on score and items in your CR - depending on scores/factor they can be very little documentation required. I've seen 1 pay stub and 1 tax return (most recent) maybe a bank statement and maybe funds verfication...
Manual is used when auto doesn't approve or gives the manual review needed response. Some factors trigger an automatic manual - like collection, late pays (recent) etc....
I know there are a few banks that only do manual - but most want to go thru the automatic (they want to be able to sell the loan so it needs to meet the guidelines).
Banks that do not sell their paper are usually more lenient on manual (at least use to be) but you may get a higher rate for this privilege.