This question is a little broad, so pardon my general answer. The TV displays whatever it is given. So if your equipment is capable of transmitting HD video in only 720p; it'll display 720p, not 1080p. Furthermore, the factory settings for the image colors are considered the best general purpose settings. If you want to play around to what you like the most, feel free.
Now for 3D, it's best to watch 3D Blu-ray discs and other media that was designed for 3D. That said, you can use a conversion feature on your TV for 2D images to be interpreted into 3D: http://www.samsung.com/us/support/supportOwnersHowToGuidePopup.do?howto_guide_seq=5290&prd_ia_cd=N0000058&map_seq=60951
I just purchased a Samsung un46eh6030f 3-d tv and would like the best advice on how to set the picture settings to watch crisp and clear hd programming and play Xbox in regular and 3-d!!any help would be much appreciated!!