The main reason you should have the shutter glasses on while calibrating is because shutter glasses tend to make the picture look a little dimmer (the lenses are, after all, alternately blocking light), and so you may need to up the brightness and contrast controls on your TV.
Most 3D TVs have 3D-specific menus, which offer from 2 to 20 options. Some of the common options include depth level (you can change how much depth you see in the picture, from nearly flat to telescopic), 3D mode (or "force 3D," for turning 2D pictures into 3D pictures), and picture modes (including split modes).
The last option is particularly important. We found in our tests that Comcast's ESPN 3D shows up by default in a horizontal split-screen mode. You can fix such an issue by going to the 3D-specific menu and choosing the horizontal split-screen option, which apparently cancels out the default split-screen and gives you a single-screen picture.
What to Watch
All right, now you have your room and your TV set up (as best you can) for optimal viewing. Go ahead, grab a Coke and a bag of popcorn, settle down on your couch, and watch...what?
As we've noted in the past, one of the biggest issues with 3D TV is the utter lack of content. But don't worry--that should be changing soon, as a slew of movies will be released in 3D Blu-ray this holiday season and next year. Until then, you're stuck with what's in stock right now.
3D Blu-ray Discs
Don't expect to see the awesome 3D feature films that are hitting theaters right now--many of them won't be available for 3D home viewing initially, or will be part of an HDTV or shutter-glasses "bundle." Currently you'll find three categories of 3D Blu-ray discs available: kids' movies, Imax- and National Geographic-type documentaries, and films whose only saving grace is the fact that they are available in 3D.
Make sure to check Blu-ray discs before you purchase them--I ended up buying Monsters Vs. Aliens and National Geographic Sea Monsters from Amazon, but both were in red-and-green-glasses 3D (paper-and-cellophane glasses included), not shutter-glasses 3D. Check for a note or a sticker on the package that says you must have active-shutter glasses in order to view 3D content.