How to enter a discounted fee after the discount date for an event
One way to handle this involves using a price set. Insert a price field with the value of -1 called Discount that is visible only by Admin. This allows you enter a discount to registrations entered in the back-end without affecting the front-end pricing. 

I believe the only way to do this without using a price set is to change your advance discount date, enter your mail-in registrations, and then reset the date. This does run the risk of people getting the discount rate if they register while you are entering the mail-in registrations.