Go to Inspections --> View Inspections
From here you can click on Actions -- Apply Coupon (or click the Coupon icon if you're using the icon view)
Alternatively you can click the 'i' Icon to go to the order info screen:
And click Actions -- Apply Coupon
The coupons that you have set up in your ISN will appear under the Apply Coupon drop down, which will also allow you to select what fee the coupon is to be applied to:
Hit Apply Coupon and you're done.
Remove a Coupon
Clicking the 'Apply Coupon' option again will allow you to Remove Coupon or add another one.