You're right about the paying the 50 first, then the remainder, but i wasn't even aware this was an option. After gettign in touch with the right people at my school, they told me that this was the way it should have been done. There was initially no mention of paying the first year AMF though (at least that I'd seen), but I knew they'd pay for the test. By the time I'd gotten the email with the 50 dollar reimbursement, I was already endorsed as an SSCP. It took less than a week for all of that to go through, and a little over a week to get the AMF payment email.
In the end, i managed to find the solution with WGU. I paid the cost up front and they issued me a check to reimburse me. So it all worked out fine in the end
If anyone else is in the same position, I'd highly recommend not doing it the way i did and just pay them in separate steps as was recommended above. It made the entire process unnecessarily complicated and there was some wording in the reimbursement form that made it seem as though this is not something that is always approved.