How are 3D movies made?

I’m still curious about 3D movies. From my earlier question the majority of people dislike them. I asked a friend at dinner last night, and apparently there are movies made specifically for 3D and others that are just made into 3D. Those marketed heavily for 3D are apparently somehow superior. Yes?

So. Is the filming process different for movies intended to be 3D movies? Or is the 3D effect always done post production in editing and it’s the same either way? Are there different levels of 3D quality? Like when I went to see Xmen recently the lines were still separated towards the end of the screen. Was I just sitting too close? Should you sit further back than you normally do to better take in the whole screen?

Any input into 3D creation and quality is welcome. Thank you!