Footwork,footwork,footwork. Check out Catching Coach's website and you'll get a good synopsis.
A trick you can use that may be helpful is simply set up a bit deeper behind the hitter, about one foot. It will help you clear the hitter easier. Be smart...will work with FB but not a curveball to the outer half.
Check your weight distribution after you come up to throw...if you are throwing in the dirt I'll bet money you have too much weight on your front/lead/left leg. Often caused by bad footwork and coming up too upright...stay low and be smooth. Drive your left shoulder down as you throw so you don't airmail into LF.
Unless you are a big kid and/or the batter is small, usually your best bet is to avoid trying throwing over the hitter. Smart batter will stand tall and not move...seen more than one broken finger after hitting a batting helmet with the throwing hand.
Watch the hitter...sometimes a hitter will move way back in the box if the steal is on in order to help the runner.
You are not by yourself in this...alot of catchers are great throwing to 2nd but struggle going to 3rd.