I already paid my tuition fees last month, but I need to change my timetable up so do I still need to accept the payment agreement? When I was shown the new payment agreement after I changed my courses it said I had to pay this much amount even though I already paid...?

Do it anyway, it doesn't hurt! Otherwise, contact accounts and cashiers and ask them. I'm not too sure how it works if you pay early, but I would imagine it doesn't really matter at this point.