First, please allow me to thank you for your service to our Nation!
Next, the Aimpoint is best used when coregistered with the iron sights. That is, when looking through the properly sighted-in Aimpoint, the dot is on the tip of the properly sighted-in iron sight setup. This is easy to accomplish for the AR-15/M16. ARMS provides a spacer to raise their M68 mount for the Aimpoint up to the iron sight line of the AR015/M16.
The Aimpoint was not designed with the M!4-type rifle in mind. There is no standard for the M14-type as to the height of a scope mount or forend rail with respect to the bore axis. I'm unaware of an Aimpoint mount that's designed for iron sight see-through. That doesn't mean their isn't one, I just don't know about it. In any case, the M14 provides a challenge in terms of buttstock comb height. To get a solid cheek weld with the Aimpoint requires a higher comb than for the irons. That's one reason the Sage and Troy stock systems which we (
Fulton Armory) offer have adjustable buttstock combs.
'Bout the only way to be able to use the irons and the Aimpoint at the same time (or rather, have them available for use without removing the Aimpoint) is to use a 45 degree forend rail. The Aimpoint is mounted on the angled rail; for use at close quarters, the rifle is rotated 45 degrees CCW so as to bring the Aimpoint around to the line of sight. Otherwise, the iron sights can be used in the normal fashion. We have such a rail available for our M14 and M1 Garand
Super Scout rail handguards.
Sighting in with your setup is no different from sighting in any optic. While the height of the optic will have a minor effect on a 50-yard zero, for example, there's no reason for the shooter to even be aware of the optical axis' height over the bore axis (except in the case of extreme close quarters, when the shooter can see over the top of a barrier through the sights, while the muzzle is below the top of the barrier. Taking the shot will have some startling results).
Regards,
Walt