Hi Sambhav
AppendixG ASHRAE 90.1- 2004: states to model base case ,if roof is present with insulation on above deck only.only need put in a simple U-value for the Specification method?. You then create your actual construction in your Proposed case.
This is to avoid "Attic effect"?.Insulation on inside of roof creates attic effect.
?Regards,
Sanjay Cholekar