When you entered your Form W-2, you should have had a drop-down field for Box 14 entries. If you selected Charitable Cash Contribution, this would flow to your return as an itemized deduction.
If you do not select that option, the amount will not flow through the return and you'd have to manually enter it in the Deductions & Credits section.
You would not want to do both as this would be taking the deduction twice as you mentioned.