While on the NES64 you can switch between the A button and D-pad Up for jumping in games, Edwin Steiner found a clever way to mod the board in a way that will still give you those two options, but also give you a third option letting both buttons work at the same time.
He was kind enough to write a very comprehensive Howto on his process, so please go check it out if you would like to modify your board yourself, or if you would just like to see how he did it.