Not entirely sure what you are asking, but I will give a try at answering.
If you are in HS and applying for an NROTC scholarship, one cannot apply for just a 2-3 yr one. It is an application for a 4 yr NROTC ride.
Now, say you do not get, did not apply for it, or for whatever reason decide to do NROTC once you get to college (as a college programer) you can then apply for a scholarship. Depending on how much college you have completed, you will be applying for a 3,2 or 1 yr scholarship. To my knowlege, the navy will not pay for school already completed after receiving a scholarship.
Once you are already at college, all the boards are going to care about are you college grades and CO reccomendations. The reason why they don't care about you HS grades, is becuase honestly, they don't mean sh!t when compared to college grades, PRT scores and most importantly your CO's recommendation. Being that you made it into the college and have college grades to review now, the HS grades are less of an indacator of how you WILL do in college when compared to how you ARE doing in college.
If you have any more ?'s feel free to ask or PM me. Hope this helped.