I pay RITA taxes. Automatic deductions were not taken from my wages until well into the 2016 year. What figures do I use to determine what I still owe?

Make sure to enter all the city or locality information from your W-2 in the Federal return.  When you get to the end of your state return, keep going, because you will be asked if you need to file a city return, including RITA cities.  Most of the information will transfer in from your state and federal return.  You'll just answer a few questions and the RITA return will be prepared for you and will tell you what, if any, you owe.