Common mod types and how to apply them:
File-replacement Mods (files inside extracted game folder)
Custom Levels (SZS)
Texture Packs
Custom Save / Titles / Fonts
Once the patched ISO is created, specific settings in Dolphin must be adjusted to ensure stability, as modded games can be more resource-intensive than the base game.
Many mods are distributed as a single, ready-to-run file. This is the simplest method.