Don't do anything other than complete the forms and answer the questions accurately. It doesn't matter which academy submits your name, you will only have one DoDMERB exam that will be valid for all SA's and ROTC for up to two years from the date of the exam.
When another academy tries to submit your name to DoDMERB, they will see that you already are in the system. No duplicate file will be created.
DoDMERB is based in Colorado Springs and either passes or DQ's for all SA's and ROTC programs. However each SA and ROTC program runs their own separate waiver process. So if you pass DoDMERB, you are passed for all SA's.
But if you are DQ'd for USNA, you will be DQ'd for all SA's. However, USNA might deny your waiver, and USMA might accept your waiver. In fact, you could possibly even be denied by Army ROTC and be waived by USMA, or vice versa.
A side note:
It is spelled "West Point," not "Westpoint."