If this is not the desired placement, you can generate the MIG design using the default pinout and manually modify the generated *.ucf constraint file. Then, run the MIG generated mig.prj and the modified *.ucf through the "Verify UCF and Update Design and UCF" flow in the MIG GUI. This validates your pinout changes and regenerates the MIG design according to your new pinout.
For more details on when VRP/VRN can be used as GPIO, refer to
(Xilinx Answer 38926). This behavior is scheduled to be changed starting in ISE 14.1 software.