Yes, if you are adding a subscription in Salesforce, you will be able to apply a coupon, as well.
Please make sure you follow these steps when adding a subscription via SFDC:
1) From a record in the Recurly Accounts custom object in Salesforce, click "New Recurly Subscription":
2) You will be presented with a custom Visual Force page that will allow you to enter Plan details, amount, add-ons, coupon discounts and dates just as you would within the Recurly UI.
