To answer your question, yes they will know you have already paid. Remember payment goes straight to home affairs and has nothing to do with FNB.
All you have to do now is go to a branch and complete your application with biometrics. Thats it.
Seems you guys dont have enough branches in Cape town, I just tried to book for all branches in cape town and all slots are taken for the next 30 days
Only places where you can get slots are Vredendal, George, Robertson and Ceres. Ceres being the closest if you dont mind the drive.
Also you...