Checks are considered "cash," so you'll enter them by clicking on the Federal Taxes tab, then Deductions & Credits, then scroll down to Charitable Donations and click on Donations to Charity in 2016.
You'll be taken to the Let's enter your donations one at a time page, and you'll see choices for the different categories of donations (Items, Money, Stock, Mileage & Travel Expenses). You'll select "Money" to enter any cash donations, including checks.