If you want registrars to be able to choose from active coupon codes within your system, rather than mandate that the codes be typed into invoices on your admin site, do the following.
From the left nav panel, select 1 Configure | Preferences. Scroll to the Preferences section and notice the line item that reads 2 Require manual entry of coupon codes for in-house registrars. If you don't want them to enter the codes manually, this should read no. To change this item, and any items in Configure | Preferences, click 3 Edit. Make sure this line item is not selected and save changes.
Now when a registrar is working with an unpaid invoice, if there are active coupons in the system, and if any rules applied to the coupon are applicable on this invoice, the registrar will be able to apply the discount by clicking 4 Apply Discount, selecting the 5 Discount Code from the drop down and clicking 6 Apply to Total.