I am having some difficulty with my shooting form and need some advice.

Set up: PSE Dakota 55lb draw with 65% Let off, WB rest, Carbon shaft with 90g tips, peep sight, kisser button, string leech and string loop.

Problem:
When shooting I have a difficult time with my " AIM"
It feels like a constant strugle between me and the bow. I draw back, anchor the kisser, get the sight pin centered in the peep with no problem. Where the problem comes into play, is putting the pin on the target. As I raise up to place the pin on the bull eye I feel like the arrow is going to sail way over the target but in reality it will hit right on the money. My eye tells me that the pin is on the target but my brain says you are way to high. I am not sure if it is a mental block issue, a form issue or just a practice issue.

Is it best to shoot with both eyes open or just one looking through the peep?

This is rather difficult to explain in words so I hope it is enough to get the picture across.