Do u mean N64 emulator for GameCube or N64 emulator for PC? If for GC, get Zelda bonus disc, and replace zelda.n64(or something similar) file with N64 ROM u want, with GCtool, and done! If u use DVD, then use fstfix to fix the image. If emulator for PC, search Project64 with Google.
Quezacotl, which Zelda are you speaking of. I'm guessing The Legend of Zelda: Ocarina of Time? I have a version that is just 1 disc, and it has the regular Ocarina of Time from the N64 and then the Master quest of the same game. Is that the same disc?
Yea, it's called bonus disc, because it comes with Wind Waker limited edition. And yea, it has OoT and OoTMQ.