My take on this is if you can get comfortable clipping in that's the way to go. However, the advantage it gives you is probably only a few percent and I don't think there's anything wrong in not clipping in. For me the reassurance of having my left foot free is more important than the slightly more efficient I'd be
on hills if I could pull on both sides. We're talking about endurance here not sprint speeds so I'd go with whatever makes you most comfortable on the bike.
Here's some Petersen "cool aid". I don't buy all of this, like I don't buy over priced tweed bags, but it's food for thought.
http://www.rivbike.com/article/clothing/the_shoes_ruse