I called my rep and they said that the referer can submit the referral card, and once that is processed, the new customer can create an account online. Then the backend team in reviewing the application will check for referrals and apply them. You just have to make sure all the details are right on the referral card.
I'm not 100% if my rep is correct but this is what I was told. The key it seems is getting the referral into their system before the new application is made, and getting the backend team to check, which may involve some calling in after the fact.