Like Marvin says, it depends on what's most important at the moment however the big benefit of auto-survey is that the survey ships know where the anomalies and you don't so using auto-survey gets you more anomalies and sooner than you could do yourself.

The only down side of auto-survey is when you have multiple survey ships out they tend to clump up and become less effective but I find that if I see that happening or about to happen I shut off auto-survey for a turn or two and direct one of the survey ships away from the other for a turn before turning auto-survey back on.

One other thing to note about anomalies is that they come in a couple of varieties. There are anomalies that are apparently fixed when the game is created and no matter when they're surveyed they yield the same outcome. However there are a decent percentage (at least 10%) of anomalies that will give you different outcomes. Therefore I always save the game before checking an anomaly and then reload and try it again and if it changes then I can use the same technique until I get the result I want.