You should look on SupportNet for information on using IOD, this forum is not appropriate for such a large subject. To answer your second question, no it cannot be used for connector pin swapping.
Questions about FPGA pin swapping are more easily addressed in the 'Ask the I/O Designer Insiders' community so I've moved your post here. Our community structure can be tricky to navigate, can't it?
You don't need IOD for connector pin swapping; it is a basic function of PADS. The pins need to be defined as swappable in the part type, so start with the help files in Part Editor.
I agree, pads and Expedition PCB have pin swapping built in just fine. I/O Designer adds a rules aware unraveling of FPGA connections on a larger scale. It also adds automation to the FPGA design process to tie together everything from HDL to schematic to layout and back. It performs layout aware optimization of signal to pin assignments, automatic updating of your connections in the schematic, auto generated part and symbol sets for your FPGA, and other cool stuff. To summarize, the supercharged Corvette of FPGA designs on a PCB.