For me, it depends somewhat on the surface — ie how much traction is available. If traction is limited, I find it best to stay seated and to try pedal with as close to constant power throughout the stroke to keep from breaking the tire loose. If traction is good, I will stand for steep, short climbs, or on longer climbs, may stand for the final portion if I feel like a really need a lower gear than what I have. But in general, I am much more efficient seated.
Hard to generalize as to whether to try avoid the obstacles on the trail — I ride a vintage hardtail, so I probably try go around things I might ride over with a newer full suspension bike, but you really just have to find what works for you, and for the particular trail.