If your documents are pushing across to QBO from HubDoc and you want the tax paid on the bills to be broken out into the sales tax module, you can do that!
You have to change the settings in HubDoc.
Go to the Accounts Menu in the corner -> Destinations
Make sure that Teeny Tiny box - Publish Tax Data is turned on :-)
Then you will get drop downs that will pick up the tax rates from your QBO database and you can set defaults.
Learn more about HubDoc.