Thanks a lot for all your help! I contacted NPC and I thought I'd post their response in case anyone else has the same problem.
"Attach both red wires from the motor to one side of your controllers output, connect the 2 black wires to the other output.
NPC wired the brushes individually to handle larger current loads."
So I think my idea to connect the wires together to make one red wire and one black wire was on the right track. That still doesn't quite answer if I can safely run the motor with only one pair of wires to get a half-power mode, but my guess is that its not really designed to do that. Hopefully my other wires will hold up since the rest of my setup uses wires that aren't as thick as the motor's leads.
Hopefully I'll get my skateboard working and I can make a post about my success.
