I was heavily involved with planning/fundraising for a central TX band last year that went to Nationals last year. The Grand Nats fees were in addition to the regular band fees for our band. The GN fees were paid directly to the travel agency that planned our logistics (air, hotel, food) for each student. The fundraising we did would be sent to the travel agency in a lump sum and then divided equally among the kids' accounts. (ex. $20,000 divided among 200 kids = $100 off everyone's balance).
There is plenty of time to fundraise for next year so don't worry. I also feel your pain about sending two kids to Grand Nats. I did that last year.