"So I have two 1099r's for the same distribution."
No, these are separate distributions and both are considered to be income. However, the distribution that was deposited into the IRA was a nontaxable rollover, so only the distribution from the IRA adds to your taxable income.
When entering the Form 1099-R reporting the distribution from the annuity (a qualified annuity, I assume, since a distribution from a nonqualified annuity is not permitted to be rolled over), indicate that you moved the money to another retirement account and indicate the amount you rolled over. TurboTax will include this amount on Form 1040 line 4a or 5a (depending on the type of qualified annuity) but exclude the amount rolled over from the amount on line 4b or 5b. TurboTax will include the word ROLLOVER next to the line.
