Its not noobish, don't worry. I was just as confused as you were only I had to go blindly through it and hope to god I didn't screw up and get kicked out of school for missing something important. Believe me, I feared that.
Anyway, when you go pick up your OSAP (which they call 'negotiating your loans') they will ask you for your personal deposit information and then tell you what the minimum payment the school is asking from you. At that point you can say "give them the minimum payment" or "give'em all I got".
You should have sent in a cheque or money order or direct banking thinger by Sept 1st with the remaining money that your OSAP and bursaries/grants doesn't cover. By the time you pick up your OSAP loan that money that you sent in for Sept 1st should be either proccessed or at least noted. I don't know about that for sure though because I've never done half and half.
Any money that is left over from OSAP will be put in your bank account (which is why you have to bring a void cheque or a banking print out... not just any print out you have to tell the teller what you need it for so they give you the right one).
You don't have to call or write anyone at the government about your OSAP, all that goes through the Financial Aid Office, they are representatives of the government working specifically at McMaster, every institution has a financial aid office like ours. They will know that your going to McMaster because when you first applied for OSAP you had to specify which institution you were planning to attend remember?
If you have any doubts what so ever you can always call the financial aid office, I've never had any problems with those ladies, they're very kind. I hope this answers your questions, if I've confused you any more I'm sorry, just let me know and I'll clarify. I sometimes confuse myself...