If you receive two letters of application status, you will see your app. ID. But it does not matter if you do not have it because the scan form to be submitted has your name, birthday, and SSN. Not a problem for them to locate you.
I had the similar situation. I sent the second copy of live scan form after me completing the exams. It is ok to send it separately because there was not such fingerprint requirement when we applied in early 2015. I recommend you send it with your application ID for the board locate your...