Before following this guide, make sure that you have installed Unity 2018.4 and you have a decrypted and extracted ExeFS and RomFS ready. Clone RTDXTools from https://github.com/tech-ticks/RTDXTools.
Before you open the project in Unity, open Data/config.yml in a text editor.
sourceDir should be set to the directory that contains your extracted ExeFS and RomFS folders.
targetDir should be set to the directory where the changed files should be saved to. You can set it to the same path as sourceDir to overwrite the original files or to an empty directory to use it with a LayeredFS (e.g. a Yuzu mod folder).
If you want to create or import custom model AssetBundles, you must first import some commonly used default textures to the project. You can do so by executing Tools - Import default textures.
The project contains all the source files generated by Il2CppInspector to allow viewing and creating all custom asset types used by the game. The output from the tool is not perfect, but the warnings should only show up infrequently and you can hide or clear them in the Unity console.