I qualify under one of the criteria. I recorded on my profile that I will request waivers and it says only an advisor/counselor needs to authorize it. So, must I write this letter or does my advisor have to write and submit it?
My understanding is that your counselor simply authorizes it through the common app system and then your common app fees are automatically waived. There is no letter to write. Your counselor should have access in your records to see what criteria you qualify under. If you want to be extra safe, as an example you could make a copy of the determination letter for free or reduced lunch and attach it to a note stating that you will be requesting application fee waivers and send it to your counselor to give him or her a heads up to authorize in your common app.