3D NES does work as any emulator does. Just right click a individual game, go to edit, then the emulation tab and use the dropdown to pick a different emulator, in your case 3DNES. You can also do this in bulk by holding ctrl and clicking on all the games you want to change, then right click one, edit to open the bulk edit wizard, click next then in the first dropdown choose emulator, and in the second the emulator you want to use for those games.