A contribution not reported on your W-2 that you make as a personal contribution an IRA is reported as any other regular personal traditional IRA contribution. Enter it under Deductions & Credits -> Retirement and Investments -> Traditional and Roth IRA Contributions and answer the follow-up questions. The fact that your employer provided you the convenience of transferring the money for you, say, as a direct deposit, is irrelevant to the reporting. For tax purposes, it's no different than having received the money in your paycheck and subsequently deposited it into the IRA yourself.
