There are two factors involved in learning to shoot instinctively:
1. Form, including body allignment, learning to draw to full draw and maintain back tension, proper grip and anchor, and a subconscious release. Form is best learned at close distances so you don't distract yourself with other aspects of the shot. Once you learn good form, it's just a matter of maintaining the same good form for every shot, whether at 5' or 50 yards. The only difference between taking a 5' shot and a 50 yard shot is that it's easier to forget good form on the 50 yard shot, since there is so much more to distract you.
2. Shoot enough arrows at enough different distances that your bow arm instinctively knows where to hold for any given shot. I like the method taught to me by my mentor, Rick Welch, where you never shoot two arrows at the same target from the same spot, unless you blow a shot and want to correct an obvious mistake in form.
Clearly, my advice is different from the advice given by Eugene above. Either method might work for different people. You pays your money and you takes your choice!