Retirement tax questions

I read your previous reply because I am in the exact same situation in filing my sister inlaws taxes. I get that the amount after death is input on the 1041. Do I record the full amount of the 1099-R on the 1040 and deduct the overage and deductions somewhere else? If so, where? On the 1041, I am confused as to where to put the deductions on the 1041 from her final payment.