The NROTC scholarship application process is separate and independent of the civilian College application process. However, if your applicant already knows they have an NROTC scholarship offer, I would encourage them to share that information with the College. My son did just that with Georgia Tech and was accepted.
NROTC is a fine program, depending on the university. My son enjoyed NROTC very much but ultimately decided that the Academy was the better fit for him. He received an appointment to USNA after completing one year in NROTC at Embry-Riddle in Daytona. Still keeps in close contact with his Embry-Riddle Mid brothers.