To handle a customer who is tax exempt from a county tax you could create a custom Tax Schedule The custom tax schedule could have the state Tax Detail, the exempt county Tax Detail (So your sales to this customer's county could be tracked and reported as exempt sales) as well as any city or local Tax Detail that may apply.
The following is a step by step example for handling a Canadian customer who is exempt from the Manitoba county (Province) tax.
After completing the above process the Rate & Boundary Import and Assign Tax Schedules routines should not affect the changes made. You should only need to undertake this process once.
If you have any other customers who are in Manitoba and are exempt from the Manitoba county tax you can repeat steps 13 through 15.