Corbin -- the DoDMERB account you created for USAFA will be the same you use for AROTC, and the DoDMERB exam you did for USAFA should "transfer" for use by the AROTC . . . I don't think you will need to do anymore as long as you didn't receive a DQ and don't need a medical waiver.
Typically, AROTC prioritizes the 4yr AROTC scholarship winners ahead of the 3 yr scholarship recipients. Sometimes that means the DoDMERB for the 3yr recipients doesn't occur until sometime during their freshman year in college, however, since yours is already done, AROTC should just use what you have already completed. Make sure you let your AROTC ROO know that you've already completed DoDMERB for USAFA. They should be able to see that on their version of the DoDMERB portal, but it doesn't hurt to send them a respectful email or make a respectful call to let them know.
Best wishes to you and thank you for your willingness to serve.