The method I chose was to use RetroArch's CLI as follows:
-f -L ".\cores\mupen64plus_next_libretro.dll" --subsystem ndd %romfile% "R:\Console ROMs\Nintendo - Nintendo 64\007 - The World Is Not Enough (USA).z64"
Just put this text in the "Extra Command-Line Parameters" textbox for N64DD (mugen64plus-next libretro core, specificially) under "Associated Platforms".