Where do I enter Medicare Part D premium payments paid directly to insurance company vs deducted by SSA and shown on Form SSA-1099?

There are two places you can enter the Medicare premiums in TurboTax.  First, when you enter your SSA-1099 to report your social security benefits, you'll see entry boxes for the various Medicare types.  When you enter your premiums on this page, TurboTax will automatically carry them to the itemized deduction section for inclusion with Medical Expenses.

You can also enter your Medicare premiums directly on the Medical Expense screens for itemized deductions -- along with any other qualified medical expenses -- by clicking on Federal Taxes, then Deductions & Credits, then scroll down to Medical and click on Medical Expenses.  Follow the prompts and enter the premiums in the Medical Insurance Premiums box.