I teach the class on how to zero the PEQ 2 and PAQ 4 several times a year, so trust me that I'm giving you good info here.
1) In order to zero an IR laser correctly you must have some sort of night vision and a bore light. After zeroing the bore light you find the correct offset target for the correct weapon, mount, and accessory then line up the laser, sighting system, and bore light to the correct point on the offset target. Since the laser, bore, and sights are all on different planes, failing to use the correct offset will mean that, depending on the range, the laser will hit on one side of the bore lineor the other. If done correctly the laser, bore light, sights, and flood light will hit at points equidistant to each other throughout their range, except as the trajectory changes due to the ballistics of the bullet.
2) HK mags have a good reputation as do magpull mags. I like USGI mags because I think the biggest problem people experience with them is that they are often just very old and have been dropped and stepped on so many times they become out of spec Even these problems are rare. I'd rather have new GI mags than used HK mags and I can getnew GI mags whenever I want.
3) A suppressor only hides the noise of the bullet when it leaves the muzzle. a supersonic bullet in flight makes a noise as it passes by you (when you've heard it you don't forget it) By hiding the noise at the muzzle, it is harder to determine the directioin that a shot came from. Using cartridges loaded to subsonic velocities makes the bullet less audible over it's path, but reduces it's effectiveness to about the same as a .22lr. Even a suppressed M16 with subsonic ammo is going to make noise from the bolt cycling, and the redused power may make semi auto functioning problematic.
4) If a laser isn't holding it's zero it's more likely to be a problem with the mount than the laser. There is no way to hold zero with a loose mount. We always have students retighten everything after firing the first 2 shots.
IR will show up fine in a darkened room with enbough ambient light to read a newspaper. leave the lens cap on the NVD and turn the laser to the bright setting.
There is no such thing as subsonic bullets, only subsonic loadings for cartridges that result in the bullet travelling at subsonic velocities. A bullet is just the projectile that leaves the barrel; not the case, powder, or primer.