I have entered a 1099-R for a IRA from my wife's deceased father that she closed. She rolled it over via check to our IRA. How do I enter it as a rollover?

After entering your wife's form 1099-R, continue the interview until you arrive at the the screen titled What did you do with the money from IRA. You can then indicate that you did a roll over of all or part of the money (see attached screenshot). The amount of the roll over is not taxable.