Courier fees and BLS Service fees are two different things. Answer to your question is Yes, you need to pay courier fees online and send BLS fees draft with your Consulate draft in the application package.
Call BLS to book for the pick-up and drop off service, they will send you a link for the courier payment over the call and you need to pay the courier fees while you speak to BLS associate. Once the payment is successful, pick up a date and time slot you think you can have your application package ready for pick up.
When you prepare for the application, include BLS fees draft along with the consulate draft in your package.