I am new to tuning bow. I have an 07 allegiance. I have had a lot of trouble with vein clearance. I have it set now to where it is shooting bullets through paper, but you can physiclly see that the rest is too low. Weird I know. I guess my question is could my problems have anything to do with nocking point. I was under the ipression that the nocking point is set at the factory and then you set your rest off of that. So can the nocking point be changed? if so how.

The nocking point can be changed. How depends on how it is set on your string. (See Greg's "How to tie in nocksets and a 'D' loop" post pinned at the top of this forum.) If it's a brass nockset I'd take it off and reset it with Greg's method using serving thread, but if you've got a good tune where it is and you have no clearance issues with your rest and fletching then for God's sake leave it alone!