The way you are positioned over the cue has a definite impact of your perception of how the cue is aligned. I had a student a couple of weeks ago who did fine on regular shots, but on jump shots, he always ended up with unwanted side spin. Once we realized that on his jump shots, his head was positioned farther to the right than on his normal shots, it was pretty simple to fix the problem. If you aren't sighting straight down the cue, or trying to sight with just one eye, your perception is probably going to be a little off. Since you normally use both eyes to see things, it's only natural that you would want both eyes working to help you sight down the cue.
Steve