In LaunchBox you have to go to manage emulators and edit Retroarch, then the associated platforms.
I guess you have one entry for Nintendo 64, using some core, like mupen64?
Add another Nintendo 64 entry but this time attach the parallel64 core, see on the picture that mupen64 is still my default.
When you are now back in your games list, right click the game, select launch with, then RetroArch and then the parallel64 core.