Normally (and I say this because it really is usually true), you do the following:
1. Make sure that you enter your state of residence in the My Info or Personal Info section.
2. Enter your 1099-R
3. After you have entered the data for your 1099-R, there will be a screen asking where this pension payment comes from.

Pick code 05E. These are the instructions:
"05E – Other Retirement Benefits – Enter the amount of retirement benefits received from any retireme..."
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