The form 1099R is entered in the program leaving the box 2a blank just like the paper form. Then the follow up interview questions are answered to determine how much of the distribution is taxable.
The box for taxable amount not determined should also be checked unless this is a CSA 1099. Unless you indicate otherwise when answering the follow up questions, the full amount would be taxable.
The full amount in box 1 is taxable, unless YOU know some reason it isn't; which you will tell TurboTax in the interview following entering the 1099-R. The only time a 1099-R is not taxable is when you made after-tax contributions to the account paying the distribution. The most common example is non-deductible contributions to an IRA.