I do an initial bore sighting in my hallway. About 15 yards long. Use a black circle. Select a diameter that appears to fill 1/2 of the bore when you look through. Have the upper secured some way so it doesn't move. Then position your head in the same place the stock would be and adjust your sights to your prefferd hold, 6 o'clock, center, or what ever. Just make sure your sights are aligned and looking through the bore. You can do this with an optic sight as well. Don't cheat by moving your head around to line up the sights. Adjust the with your noggin in the same place it would be as if the stock was attached. Next thing, go on the internet and print out a target circle, with an aiming black, about 5.5-6" in diameter, or get some shoot and see targets if you have a hard time seeing the hits. Also, put it on a brand new cardboard with no holes in it. That will make this task a hundred times more easy. Take it out to the range and place it at 50 yards. Crack open the back pin, open up the upper, and sight through the bore with the rifle well supported. Center up the black in the bore, the sights should be pretty close already. If not make minor adjustments.
Find out and know how much 1 click value is worth on your sights. That means if your irons are 1MOA per click, that will translate to 1/2" at 50 yards, or 1" @ 100, 2" @200, etc.
At this point you should be on paper and you can find tune your sights with 3 round groups.
If you are not on paper something is wrong with the gun, sights, ammo, or that nut that is behind the butt stock may be loose.
I have never used a bore sighter, and have had great success using this method. As long as you can see down the bore, you should have no problem sighting in.