You need to report both Forms 1099-R. If the pension was a direct rollover to the IRA it should have a code G in Box 7 or the 1099-R. That would automatically be reflected in the program as a non-taxable rollover. If instead, the money was paid out to you, then you will need to answer the questions after entering your 1099-R. After you enter(ed) the 1099-R, there is a page that asks "What Did You Do With The Money From [Retirement Plan]"?
Be sure you indicate first that you "...moved the money to another retirement account (or returned it to the same retirement account)." and the you "rolled over all of this money to another IRA or other retirement account (or returned it to the same account)."
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