This is the first year I've paid tuition so I wasn't sure what I was doing. I think I put the money in the wrong spot.

When you go in to pay your tuition you have the option of putting it in your student account or payment agreement. I made the first transfer (first half of the tuition) to the student account by mistake. I realized what I had done and put the second half on the payment agreement, but now my account says I still owe half of my tuition on the payment agreement while my student account has a four digit negative balance.

Has anyone else made this mistake before? Will it sort itself out September 1st when payments are due or am I going to have to go to the McMaster Financial Aid office?

It will sort itself out, the two accounts will merge together on Sept 1st. If you do want to talk to someone about it, it would be student accounts and cashiers services.