NTS handles tax withholdings like In/Out transactions. When taxes are withheld, it records the taxes on your reports like an "In" transaction. The "Out" part of the transaction occurs when the check is written to pay the taxes.
When making budgets for taxes, the only taxes that the church should budget for are the employer portion of the payroll taxes. U.S.A. Federal Income Tax is an expense for the employee, not the church so the budget for this should be $0.00. For Medicare and Social Security, the budget should be only the church's portion of the taxes. For these taxes, the church is required to pay half of the tax with the other half deducted from the employee's check. The budget should reflect the half that the church pays.