Different ways to package mods for different games
When a mod is installed with Thunderstore Mod Manager, the files might not be copied as-is into the profile folder. For example files placed in subfolders might end up getting copied to the root folder. How exactly the files are copied depends on the mod loader used by the game.
BepInEx Games
Folders
The Thunderstore Mod Manager will empty the contents of folders in your package's .zip file unless they are inside specifically named folders. The name of the folder decides where the file will be extracted to. Here are the common folder routes in most games that use BepInEx for modding (the BepInEx folder can be omitted):
BepInEx/plugins
BepInEx/core
BepInEx/patchers
BepInEx/monomod
BepInEx/config
For a full list of install rules for each game, check the ecosystem-schema
An example of a Thunderstore package having its folder emptied into the root of the package folder
An example of the Thunderstore package having its folder preserved
If you still have problems getting the files into right places, you can download another package for the same game from https://thunderstore.io/ and see how it's structured.