NYS return - Enter any Partner, Shareholder and Beneficiary Subtractions section : How do I know if I need to enter a particular code? Is there a box on my W2 ?

This is looking for adjustments from a Schedule K-1.  This information should be provided by the partnership, S corporation, and estate or trust- look for notes on the K-1 form if you have any K-1s.  

For reference, see Instructions for Form IT-225 New York State Modifications.