It depends on what kind of an analysis you are doing.
For a SOL 101, nastran treats every subcase as a separate analysis, and the displacements that you obtain would be with reference to the un-deformed configuration.
For a SOL 106, having multiple subcases would mean that the deformed configurations from the previous subcase would be the starting point for the next subcase ( i.e. updated structural stiffness is passed b/w subcases)