In the both versions of the Zelda 64 Engine, the data for each individual location of the game (for example, Inside the Deku Tree, Hyrule Field, Zora's Domain...) is stored inside of scene files. The scene file more or less contains references to all of the data needed to generate a location that can be explored, and the links (or exits) to the other scene files.
More important however, is that the graphical data and actor lists (collections of objects and NPCs) for each scene is broken down into one or more map files (for example, each room in a dungeon is one map file), which allowed the designers to create bigger and more complex scenes that would appear to have no loading zones, and minimal lag.
Under normal circumstances, only one map file is loaded at a time. However, if you hover so that you're in the area of an unloaded map, and walked back in bounds through the map loading trigger, duplicate copies for the actors in that map will load.
This can be used in several areas to clone certain NPCs. For example, you can do this in the Lost Woods to clone the Skull Kid that you would give the Skull Mask to, allowing you to obtain several extra heart containers.