Yes after you enter the 1099R the next screen will ask Do any of these situations apply to you with a list. The 7th item is "I transferred all or part of this money directly to charity". Check that and the next screen will be either for RMD info or ask how much was transferred to Charity. Just keep going though all the screens.
Then do NOT enter it again under Deductions & Credits. It only goes on the 1099R entry. Otherwise you would be deducting it twice.