No, you would enter $6000, the full contribution amount in Box 1 of the 1099R to match the excess contribution amount you made originally. .
To begin reporting the contribution amount that was returned to you, go to Federal > Deductions and Credits > Traditional and Roth IRA Contributions.
As you proceed through the interview, the program will inform you that your contribution is too high. Then the next screen will tell you you have a penalty but then will allow you to enter a contribution amount withdrawn before the due date of your return. Here you will put in the full amount of the contribution, which is $6000.
@jdlavian
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