Sorry, I wasn't being clear. I submitted yesterday.
You pay the $90 and then you "are submitted".
You go back to the original link that prompted you to do the secondary, and you re-enter AMCAS ID and DOB. From there, it'll take you back to a page where you can look at your essays and secondary etc, and it'll say "APPLICATION INCOMPLETE" and it will tell you to upload a photo, and you'll be able to "choose file" and "upload photo" straight to that page.
Long story short, pay the $90, log back in, and you'll see where it tells you to upload the headshot.
I hope that helps you!
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