It sounds like you are confused as to what NAPS is. It is NOT a back door to the Academy, nor is it an easier route, or a way with lower requirements. The purpose of NAPS is to allow the Admissions Board to give someone who has all the qualifications to enter BUT who is weak in some academic area. If the board feels with some prior tutoring and study on their part, they can be brought up to speed with every other candidate entering, they MAY be offered NAPS to get up to speed before entering the buzz saw of Academy academics. If your grades stink now, NAPS wouldn't save you nor would it be offered. You have to be close to begin with and have a lot of other fabulous qualities that other candidates who do meet the academic standards don't have.
NAPS has also been criticized in the past for being a pool of athletes too dumb to get in without tutoring and usually somebody is pointed to as justification. That is not true nor is it entirely false but any athlete with a great throwing arm still needs to be very close to the Academy academic levels to be looked at as the Navy absolutely detests losing people for any reason, academics included. A hole in the class and in the fleet is created that cannot be filled until the next year.
You need to concentrate on getting an appointment from the git-go and look upon NAPS as a rare blessing if you don't. Good luck.