If you already requested and was granted a waiver by the IRS for the late 2015 RMD distribution, there is no need to file Form 5329 to request the waiver again. Simply report the combined distribution on your 2016 tax return by entering the Form 1099-R.
If the IRS is instead instructing you to file Form 5329 to request the waiver, it's a 2015 Form 5329 to request the waiver that you must file separately from your 2016 tax return.
