After a couple emails with Andy @ Ultimarc and these posts I was able to solve my problems here and wanted to share with the group in case this is helpful in the future for someone else.
The main thing I found was to NOT use the "panel" view within WinIPAC and instead use the "table/grid" view of the mappings. Also on an Win & machine MAKE SURE you run the WinIPAC software in administrator mode or you will not be able to program the mappings to the board.
I created a big hand written grid off all of my ports, and the buttons attached to them to begin, then for each button i wrote out what key on the keyboard I would be mapping it to. This was VERY helpful.
I then plugged in the first IPAC2, opened WinIPAC in admin mode, and mapped all the buttons based on the chart i created. I then clicked "program" in WinIPAC and all the buttons saved. I then unplugged this board, plugged in the other, and did the same thing.
After both boards were programmed, I plugged them both in, and you can then use your chart you already created to map the specific buttons to use in each emulator.
I am still having some issues however with phantom button clicks (i think one i mapped to "escape" is someone triggering while using an emulator and it's closing windows, showing the toolbar, etc, so i need to figure that out next). I hope this is helpful for others!