Depends what you want to do and how many survey ships you have kicking around. I find it's more useful to use the survey ship on manual at the start of the game, because it's good for scoping out star systems to find habitable planets. If I can scoop up some rocks on the way, that's good too.
Later in the game when I'm looking for a research boost on a long project, I might direct one or two towards civ graveyards.
But yeah, auto survey is fine, it even seeks out anomalies in unexplored parts of the map.