The allowed deduction is for the business-use percentage of the lease price plus regular expenses (gas and so on) minus a small adjustment (the lease inclusion amount) that is smaller this year than in the past.
Your Form 1099-R, which you receive from your IRA custodian, will not reflect anything other than a distribution, so you will need to make the adjustment on your tax return, deducting the amount that was distributed to the charity from the taxable IRA distribution amount (line 15b on your Form 1040).
The IRS has a withholding calculator that can help you determine the correct amount, (click here.) If you make an adjustment, be sure to capture the increase in your paycheck and put those dollars to the best use, whether it is setting up an automatic transfer from a checking to a savings account or increasing your retirement plan at work.