They are separate application processes and you apply to them independently. The NROTC application requires that you list 5 colleges you would like to attend with NROTC units. One of them must be a public college where you are entitled to in-state tuition. If you are awarded a scholarship it will be to 1 of these 5 schools (there are some exceptions but they're too weird to even bother discussing here). It is your responsibility to apply to and get accepted by the colleges. Sometimes folks are awarded scholarships to a college that has not accepted them and they therefore lose the scholarship if they are unable to transfer the scholarship to a college where they have been accepted. Choose 5 colleges that would be a good fit for you. I even recommend choosing them in the same way you would chose them if you were not applying for the scholarship.
Do you plan on applying for Navy Option, Marine Option, or Nursing?