The menu at the top and bottom can be toggled by clicking the red cat head at the upper right. The cursor can be toggled with the up key. If it's missing, you can get it back by mousing off the flash and back on it. The bottom option just turns off one of the images.
I recommend the Cross-eyed setting, and crossing your eyes so that the two images form a center fully 3D image. But be sure to uncross your eyes when it ends.