Can I just pay the difference between the taxes for the county I actually lived in and the taxes for the county my employer withheld? They are different counties.

My employer withheld taxes for the wrong county. If I select the county I lived in (not the one my employer withheld) my state tax shows the full amount. If I select the county my employer withheld tax for, the amount they withheld is subtracted from the state tax due amount. My employer said I could just pay the difference, but I don't see how to do that with Turbo Tax.