My experience has been that the router does not do a good job of picking the best channel. I have seen it pick the most congested channel on numerous occasions.
By setting the channel manually, you know for certain the router is on the least congested channel. The downside is that channel congestion changes over time (neighbor adds a WAP, or neighbor's router auto-selects the channel you're on).
So turning off auto-select really depends on how you want to manage it. If you want to set it and forget it, I say leave it on auto-select. If you want check that you're on the optimum channel periodically or when speeds seem to go downhill, then go ahead and pick a specific channel.