For me they did not charge. I applied through them only.
and advantage of applying through them is that I did not have to pay application charge for any college.
If you are capable enough to apply by your own so just go on.If you have confusion regarding anything you may take help of consultancy.Remember one thing they(consultancy) won't issue your visa.All depends upon your profile and visa officer.
If you are in canada. then personally go there and talk with them.
If you applied through any agent, better ask them. they will take care of your problem.