The 2016 contribution should be entered in the IRA contribution section and marked non-deductible (if it is not automatically nondeductible because of high income). That should account for the 2016 contribution.
The 1099-R interview (after the 1099-R entries screen) will ask of you tracked your non-deductible contributions - says yes, then enter the 2015 contribution. Then the total value of all existing Traditional, SEP or SIMPLE IRA accounts at the end of 2016 which if not zero the conversion will be partly taxable since the nondeductible basis must be pro-rated over the conversion and year end value.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
