This stuff confuses the heck out of me, and no other threads that I searched for could give me a good answer.

Summary:

-My tuition for the year is $ 8326.70
-I chose osap flex plan.
-Osap's estimate is $9,680
-Based on my osap estimate, they deducted $ 4996.02 (60% of my tuition)

Shouldn't they have deducted 60% of my estimate? (5808) It's weird because it says I still need to pay 1260 in my student account..

they usually deduct 60% of tutition fees not the estimated amount.
the other 40% of tuition (if osap is covering 100% of your fees) will be paid in the January semester.
in some cases, the osap estimate will exceed the total tuition fees of that academic year and the leftover money you can pretty much do whatever you want with it. ie. put it towards a saving account, make repayments to nslsc, use it towards summer school or rent or other school related things or even blow it on stuff you don't even need.