I find that i tend to set it up and throw the kick when I've got the opening...where the kick lands tends to become more irrelevant (not totally).
Typically, I like to throw it as a counter to the roundhouse or some other back legt kick that leaves the torso wide open. If the kick goes high, I tend to get the solar plexus area...a good show stopper. I usually aim for the ribs. If I'm low, I tend to hit at the belt line around the hips. This tends to hurt the opponent and upset balance/move them back. I can then follow up with other stuff. I suppose better precision will come with time and practice...but I tend just to throw it and not worry too much.
I was given some good advice from an Olympic TKD guy on how to speed up the back kick and improve accuracy. He drilled us on getting a fast pivot (without trying to lift the leg to the side and make it a weak hook kick). From there he told us to make sure that our knees brushed each other as we threw the kick. By doing this, you improve the alignment of the kick and eliminate unnecessary motion. That was the single best tip I ever learned and it improved my back kick tremendously...make sure the knees brush.
Peace,
Erik