For reporting a Qualified Charitable Distribution, you should have been presented with the Transfer to Charity? page in the follow-up to entering the Form 1099-R, presented immediately prior to the page for indicating an HSA Funding Distribution. Simply indicate the amount that was transferred from the IRA directly to the charity.
Tax only asks the charity question if the distribution is from a traditional IRA and you were age 70½ or over. For other types of accounts or if you were under age 70½ you'll need to report the distribution as a regular charitable contribution deduction on Schedule A.
