Use @meleu's joystick selections script, it allows you to choose the (player) order of the joysticks per core/system. But if you're DragonRise controllers are always USB connected, they'll probably always be js0 and js1, so I guess you can use the RetroArch gui and choose that player1/2 and joysticks on 3rd and 4th position and save the the core remapping.
For N64 though, I think you'll need to edit the configuration file explicitly if you're using the standalone Mupen64 - more details are in the docs for the emulator.
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