Are you trying to code and publish a bill to QBO and the only option you have is Extracted Amount?  If you had the option before to select the various tax codes that you have set up in QBO, it's a known glitch in HubDoc at the moment, which they are trying to fix.

To fix it yourself now, simply Disconnect the connection between HubDoc and QBO and Reconnect.  
Just remember to Click on the box again to Publish Tax Data.

Learn more about HubDoc. 

Updated: April2017