Side-by-side stereo means that the normal display is divided into two halves, a left view and a right view, each occupying one-half of the original display area. Each view displays the current molecules from a slightly different perspective, corresponding to the left and right eye of the viewer. The images are separated, however, so to actually see a 3D object you must direct your eyes until the two images are on top of each other, and then focus on the resulting image until you can see it as three-dimensional.
There are two ways of placing the images. In wall-eyed stereo, the left eye's image is located on the left side of the display, and the right eye's image is on the right. This is the standard method for displaying stereo images in publications as it works well when the display (in this case, the piece of paper) is close to the eyes. It is called wall-eyed because your eyes are directed the same way they would be if looking at a distant wall. In VMD, this method is referred to as ``SideBySide'' stereo.
In cross-eyed stereo, the left eye's image is located on the right side of the display, and the right eye's image is on the left, and hence the name cross-eyed. This is mostly used for distant displays (such as overhead projections) as it is much easier to cross eyes at that range than use the wall-eyed method - you are already looking at the wall. In VMD, this method is referred to as ``CrossEyes'' stereo.