The one shot zero is simply a freeze function. It locks/retains the image on the screen and then allows the user the ability to move the axis point to your point of impact. What gets confusing is Pulsar uses the term distance value a lot.
A pulsar scope has multiple profiles and multiple distances. Those distances don't have to be distances, they are simply another X,Y coordinate values (POI value).
For instance, If you have 3 guns (204, 22-250, and 308) you could use Profile A, Profile B, and Profile C. Another option would be to use Profile A, and use distances 204, 250, and 308. That may be easier to remember than which gun is A, B and C.
Distances can be used to allow a user the ability to have a 100 yard, 200 yard, 300 yard zero if you want. However, Crazyyote, as you are saying, many people will just want one zero, like a glass scope that is for instance 1" high at 100. So, in your case, you will adjust the crosshairs so your aiming point is slightly lower (down) than your target. It seems opposite of sighting in a typical glass scope. If want to raise a glass scope POI, you turn the dial Up. On a thermal, you are moving your crosshair, so you move the crosshair down. This will cause the shooter's POI to rise.
As far as amount of distance for each X,Y value, it can depend on model, etc. However, all the Pulsars I have used when you are in the zeroing function, there is a magnification option. This allows for the ability to move the crosshairs in increments of 1, .5, or .25. This will allow for minor adjustments if necessary to your POI. 1 seems to be slightly more than 1 MOA, but with the finer adjustments, you should be able to get it where you need.