The application processes are completely separate and independent. You submit an application for the NROTC scholarship and then to the schools you wish to attend. You will list schools on your NROTC application and a scholarship will be awarded to one or more of the schools you list on your NROTC Scholarship application. NROTC scholarships are awarded "blind" with regards to college acceptances. Make sure that you list a few "safe" schools on your list. You will have an "application coordinator" that will work with you during the application process, but it is not the same as a BGO.
Good luck!