If you want to use a Flat Rate Box or Envelope you have to buy specific postage. For example, if you want to ship a Small Flat Rate Box, you have to buy Small Flat Rate Box postage.
To access this type of postage in Pirate Ship, just click the Type of Packaging dropdown when you're creating your labels and select the type of Flat Rate Box or Envelope that you're using:
You can get free Flat Rate Boxes and Envelopes at your local Post Office, or you can order them online and have USPS ship them to you for free! Just go to https://store.usps.com.