If the customer's account isn't active yet:

When you go to manually activate the customer's account, you'll find the option to apply a coupon code on the same window: 

If the customer's account is already active:

Visit the customer account you'd like to apply the coupon for, and you'll find the option under the Plans & Billing tab:

Note: Coupons applied to an active account will apply on the next invoice/s they're issued; they will not apply to any invoices that were created before the date on which the coupon was applied to the account.