A script is simply a file with a .zs file extension, that is all that is needed to classify a file as a script file.

Windows hides the file extensions of "known" file types, this means that text.txt may show up as just text on your machine.

This also means that script.zs.txt will also show up as script.zs on your machine.

If you are unsure if file extensions are shown or not, take a look in your game directory and find the file called options.txt, if you see a file called options and not options.txt, that means that your file extensions are hidden and you may have trouble when making script files.

You can find out how to fix this here.

Generally scripts go in the scripts folder of the install, it is on the same level as mods, config and logs.

If you're having trouble finding it, you can run the /ct scripts command in game, and it should open the scripts folder (This only works in single player, as you can't open a folder to the server scripts folder).

A tree view of how it should look is like so:

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├── config
├── defaultconfigs
├── logs
├── mods
├── saves
└── scripts

Scripts inside the scripts folder can be in any number of sub folders, an example of this is putting scripts into folders based on the mod, here is a tree view of that:

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scripts/
└── mods
    ├── botania
    ├── recipes.zs
    ├── tags.zs
    └── thermal
        ├── recipes.zs
        └── tags.zs

That is perfectly valid and is a great way to manage script files in a large modpack!