lisahcpa,

You are correct, NY does not conform to Federal depreciation rules and the CT-399 must be prepared to report the NY depreciation amounts for assets that would be impacted.  

Information should be flowing through from the federal return if completed correctly.  

Please navigate to the Asset Entry Wks on the Federal product and confirm the assets are correctly sourced to NY in the State Depreciation section of the Federal Asset Entry Worksheet.  The program will determine the conformity of the asset to federal depreciation in this section and recalculate depreciation if necessary for the NY filing.  I have attached an example of what the entry on the federal return should look like for a asset that qualifies for 100% bonus depreciation.   See attachment.