You have two primary options when it comes to enemy shuffle: overworld enemy shuffle and palace enemy shuffle. You will never find palace enemies in the overworld or overworld enemies in the palace, unless the game normally allows for an enemy to be in both (like bots).
For the overworld, East and West Hyrule have different enemy sets. This means that you will never see enemies on both continents, unless the game normally allows it (like bots). You can find a list of overworld enemies and their locations here.
For the palaces, palaces 1, 2, and 5 share and enemy set, palaces 3, 4, and 6 share an enemy set, and palace 7 has an enemy set of its own. This means you will never see Doom Rattlers in palace 4, but you might see Magos in palace 1. You can find a list of palace enemies and their locations here.
Enemies are put into four categories: large (sprite consists of two or more tiles), small (sprite consists of one tile), flying, and generators (rock generator, bird generator, etc.). Enemy shuffle will normally not mix enemies across groups.
If the Mix Large and Small Enemies option is selected, mixing between the large and small enemy groups will be allowed. This means that bots can be replaced with dairas and vice versa. Because of the difficulty of this option it is not recommended for new players.