Peter here from Shopify Support!
When setting up your taxes, you'll have the option to either manually enter in the country and state tax for each state, or you can have your taxes calculated automatically. If you go with the latter, then it should only add your physical location states taxes which would include state/county/municipal rates. To get this setup, you'll want to head to Settings/Taxes, click into "United States" then select "Calculate Taxes Automatically."
Let me know if you run into any issues!
All the best,