You may have to pay for both temporarily, depending on how you choose to resolve the issue. But you won't ultimately be paying for both products in the end since you can either get a refund for the CD, or Customer Support might give you a service code for the Online product instead, depending on how they want to resolve it. Here are a couple of options:
If you bought a CD you can't use, you could pay for your online product and submit a refund request for the CD. Or you can speak to TurboTax Support for a remedy. This is their busiest day of the year, however, so they could be hard to reach.
I don't know how Customer Support would choose to resolve it. They "might" provide you a service code for your Online product, which might be a better deal for you, since the Online product is often more expensive than the CD. Or they might also say to pay for the online product and refund your money for the CD.
If you can't reach Customer Support, you could pay for the Online product, then you can use this online refund request for the CD.
https://support.turbotax.intuit.com/forms/refund-request.jsp
Or to speak to someone at Customer Support for a possible different solution:
Use the form at the link below to schedule a call back, or it may provide a number. Hours are 5AM-9PM Pacific (8AM-12 Midnight Eastern) 7 days/week.
When the form asks what product you are using, go ahead and say "CD/download" in the dropdown menu, since that's what you bought. And by indicating that product, that will be the most direct way to the right department.
In the issue field, just say something like "billing issue. purchased wrong product" but without quotes.
https://support.turbotax.intuit.com/contact
