When you enter the 1099R in the income section, TurboTax will ask what you did with it (rolled it over or did something else with it) and you will answer the rolled it over.
Then TurboTax will ask if you rolled it "all" over, and you will answer --some of it, and then enter the amount you rolled over.
You will then be taxed on the amount not rolled over.
Just enter it and follow the questions.
