Keep doing it for several minutes. Try standarizing the height of the toss, making each one send the ball at more or less the same height and location. With a little practice it should be easy to make the ball go up and down monotonously. Eventually, that rhythm will help you tell where balls are in the air, just as surely as your eyes will. This might take a while, but it'll come.
People often wonder which ball a juggler looks at when juggling.
He or she is usually not tracking the motion of any particular ball, just trusting to peripheral vision to get a working sense of them all at once. This is one of those Zen-like observations that can make a huge difference in understanding what juggling is all about. You cup your hand to toss and it stays cupped for the catch. The position for both is essentially the same. Because as soon as you start juggling, you'll find one ball coming in for a landing just as you've given another its flight.