I just spoke with a colleague who has been accepted to Jag. She said that there is no application fee, but that the 200 Euro fee is considered a confirmation security on the seat, and is payable only after you are accepted into the program.

As for payment, I can't help you. She has not committed to going, and so has not gone through the payment system. If the program is at all like schools in Germany, and I suspect that it is, then a payment through your bank is the easiest method of payment, and can be arranged by most tellers or bank managers.