mhdhamood,
IMO, by increasing column dimension in-between the slab-on-grade and the mat foundation, you are actually increasing the mat thickness, which is otherwise needed to account for larger punching.
I would (in case mat foundation is yet to be poured), treat the 'enlarged column neck' and the mat portion exactly beneath it, as a single mat (of thickness equal to sum of normal mat thickness and 0.5 m i.e thickness of 'enlarged column neck') and will provide reinforcement as per requirements of larger mat thickness. This concept is similar to what has been discussed in following thread: (http://www.sepakistan.com/topic/1689-drop-in-mat-foundation/ )
BTW... (1) How are you analyzing & designing the mat foundation? Using some software (CSI SAFE etc.) or manually?
(2) Has the mat foundation already been poured, or is yet to be poured?