There are services that are out there that will do as little as sell you lists of locations and rates to others that will integrate with your billing & CRM software and add the appropriate tax to the invoices and then send it to the proper agencies at of the states. It just depends on how much you want to pay for what features.
It's usually worth paying for these accounting platforms, such as Bitwave. I would write a few lines of code to integrate Bitwave with the CRM/ticketing system, Minerstat, mining pool sites, the exchange, and the wallet API for payouts.