I don't use both eyes, but I can. Your brain is much less "confused" when you only use one eye, because it only has one image to line up. When you use both eyes, you have two images in front of you, but you're only trying to focus on one (your dominant eye's image on the sights).
If you want to use both eyes, it's easy after a little practice.....
1) Line the sights up on your target as you normally would, with just your dominant eye.
2) Without changing anything, open your non-dom eye.
3) The picture(s) you see is how a lined-up target should always look when both eyes are open. If you do this "drill" enough, you can train your brain to ignore what the non-dom eye is seeing and concentrate on the picture (sights and target) of the dominant eye.
That being said, to me it's not worth the hassle; I shoot one-eyed.