To change the charges, go to the Charges tab of the booking or quote (you can do it in either place depending on whether the guest has actually booked). The simplest thing to do is to add a new charges (using the plus button next to the item you want to add it above), set it to a type of Other Discount, and put in a negative amount or % (see screenshot -- click for a bigger version).
If you have discounts you use a lot, like repeat guest discounts, you can set those up over in Settings > Surcharges & Discounts and they'll be available to select in the Type box.
