In brief: If you wish to create or publish an existing discount code and have it restricted to ONLY be used on purchases of E-Certificates, simply follow these steps.
Select the Global Event Management Tab.
Select the Discounts tab on the left hand side.
Search for a current discount code in the search field and select Edit Details
or select "Add New Global Discount" to add a new discount code.
Name the discount code, and select "Yes" to the question "Valid on E-certificates"
Once you select "Yes" a new option will populate, and you can now select "Yes" to "E-certificates Only" to have the discount code restricted to use on e-certificate purchases only.
If you would like to test to see if the discount code works on E-certificates, simply navigate back to the E-certificates page in Global Event Management, select the e-certificates link/Sell E-certificate button and enter the discount code into the discount code field during the purchase process.