Unfortunately, Freescale is not in the list of supported vendors for I/O Designer and I/O Optimizer. At this time, we only support Xilinx, Altera, Actel, and Lattice so you'll be unable to use these tools for managing the i.MX6. Your best bet for now is using Symbol Wizard and Library Manager - I recommend using File > Import Pins to bring in a CSV file to help create high pin-count fractures.
We are aware that these types of semi-fixed IC's are overlooked in the flow. I have heard we are looking at adapting some of our current tools (I/O Optimizer, Package Integrator, etc.) to create a mid-tier solution which can handle these types of devices - stay tuned for more info.