Thanks for the responses.
I guess my main issue with the new software is you can't see what anything is. Your screenshot in the website shows what connection is what, but that program doesn't do that, so you have to go through the drop-down for each item. It would be nice to just click on the board and say ok, i want to program p1 joystick, here's up,down,left,right. But i don't have a clue what connection on the board is actually p1 joy/buttons, etc.
I think my issue is something with USB as both controllers can't be plugged in at the same time. I'm going to try another computer tonight, or put in another USB controller.