First off, no question is ever stupid. If you don't know its fine to ask.
Anyways I hopeI can explain this in a way that makes sence. Typical vs. Non-typical really only matters if you are scoring the deer. When you score a typical deer, you add all of the normal points (ie: ones that are upwards and in a normal pattern...not coming off of other points and such). Then you go and subtract the the unique points (ie the ones that don't follow a normal pattern).
Now when you score a Non-typical rack...instead of subtracting those abnormal points...you would add them. I think that makes sence and is basically correct.
As far as I know you are allowed to enter any deer in either book...just the deer that are more typical will score better in the typical category and the non-typical deer will score higher in the non-typical book. Because of the fact that you can enter them in either book that is why some deer look quesionable.
One other point, when I say add the normal or abnormal points I don't mean to add 4 if its a 4 point...you must add the
inches of each antler. In addition you need to add the circumference of the antlers in specific locations along with the inside spread and length of main beams.
Here is a link to the proper way to score each type of deer:
http://www.boone-crockett.org/bgRecords/ScoringYourTrophy.asp?area=bgRecords