Tim.. I have used them 3 times now, the last 2 being through the on line submission.
You are definitely being told incorrect information by the crew members. You have to submit the certificate before you cruise. And you can't apply the FCC you purchase on a cruise for THAT sailing. It has to be a future sailing. Submitted either via mail or the on line tool. There is a physical FCC number on the FCC. You need the booking number you want to apply the FCC to and the FCC # to redeem them online. I have bought them after I had booked a cruise (months after) and applied them to that booking but it was before final payment was due (which I think is critical if you want to do that) But if you have FCCs and book a cruise within the final payment date you can apply them to it as soon as you book, but you still need a booking number before you can submit them.
If you give me more information on what you are trying to do I think I can help.
Carnival Cruise Lines:
Fantasy 90, Celebration 95, Victory 05, Conquest 05, Spirit 6/06, Freedom 6/08, Holiday 7/08, Victory 6/09, Valor 9/09, Dream 6/10, Splendor 8/10,Conquest 8/11,Magic 11/11,Triumph 4/12,Spirit 7/12,Freedom 11/12, Triumph 2/13 - The fire cruise, Magic 1/14, Freedom x 2 6/14
NCL Dream October 2006, RCCL Mariner OTS June 2007, Celebrity Silhouette 2013