How does midas determine which moment of inertia to use for beams and columns during structural analysis? How is the post tension being resisted by the columns?(P.S. AASHTO refers to this in C 4.7.1.3.)

Actually, based on the current setting in the model, the complete stiffness of the columns is being used.  It is uncracked.  If it is required to reduce the section stiffness for any particular case, then the section stiffness scale factor and boundary change assignment features have to be used.  Kindly refer the image below and the attached model.