Depending on the mod format, you will need to package your mod differently by using folders.

Stratum mods

To create a stratum mod, check out the Mason Getting Started guide.

To build your Stratum mod, you must first make your manifest, so you might want to check out the second part first.

Deli mods

No folder needed, place your .deli file inside of your mod folder.

[Your mod name]/
    [Your Deli File].deli
    [Your Second Optional Deli File].deli
    icon.png
    manifest.json
    README.md

Sideloader mods

Place your .h3mod or .hotmod file inside of a folder called Sideloader inside of your mod folder. A .h3mod and .hotmod are identical; they just end differently.

[Your mod name]/
    Sideloader/
        [Your Sideloader File].h3mod
        [Your Second Optional Deli File].hotmod
    icon.png
    manifest.json
    README.md

Asset bundles

Place your assets inside of a folder inside of your mod folder called LegacyVirtualObjects/.

[Your mod name]/
    plugins/
      LegacyVirtualObjects/
        [Your assetbundle file]
        [Your assetbundle file].manifest (optional)
    icon.png
    manifest.json
    README.md

TnH Music

No folder needed, place your .bank file inside of your mod folder.

[Your mod name]/
    MX_TAH_[MyEpicMusicModNameHere].bank
    icon.png
    manifest.json
    README.md

Now that your files are compiled together, zip your files together and head on over to Thunderstore to upload your mod. Make sure to log in, then press the Upload button in the top left. Set it's category, drag your .zip, and hit upload.