Did you mistype something? Sighting in from 3'? This isn't going to affect anything so fas as sight settings are concerned. 3' can , for all intent and purposed be considered dead flat. What you should be doing is standing on the ground to sight in. Get a pin or two sighted and then get up 15' to 20' and shoot to see what your point of impact is at your normal distances.

The trick to shooting from an elevated position is to draw the bow just as you would on the ground and then bend at the waist to execute the shot. If you keep the upper part of your body in a "T" shape your shots should still hit as they do on the ground for a given distance. This is something you have to practice till it becomes second nature.

If you don't bend at the waist and just drop the bow arm the chances are that you'll shoot high. The whole upper body form is changed, which changes your draw length and changes the angle at which you look through your peep and see the sight pins.