Go back to the 1099-R interview and do this:
Enter the 1099-R, including box 2a.
Skip through the next screens until you are asked if this is a qualified plan. Enter that it is qualified plan (but see this OPM page).
On the screen that asks about periodic payments, answer "yes" (this was not a one-time payment, was it?).
Answer "yes" or "no" on the next screen, depending on whether you started the pension this year or not.
On the next screen, if you answered "no", it will ask you if the amount in box 2a was used as the taxable amount - answer "yes", if that is the amount of the distribution less the basis. (remember the return of basis is spread out over the life of the pension).
If the next screen is because you answered "yes" to the first year question, then probably the box 2a amount has been entered in "I will specify an amount". If not, then put the box 2a amount there.
Look at your 1040 - the box 1 amount on your 1099-R will be in line 4c, while the box 2a amount will be in line 4d.
Note that there may be other pension amounts which are included in these lines.
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