I don't really know anything about the N64, but I suspect that, being a 3D system, that it might not even have any sort of display layer system. It would be left to the game programmers to code their own layering system. Anyway, it's just my impression given that no such option exists yet in a N64 emulator.
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Current projects: Metal Storm (NES), Clock Tower (SNES), Ristar-The Shooting Star (Gen), Sonic The Hedgehog (Gen), Sonic CD (Sega CD), Mega Man Zero (GBA), Battletoads (NES), Bucky O'Hare (NES)