If you want to make the preset or other really simple and straightforward mod to install via a mod manager, create the archive with the folder structure intact, more advanced mods require installer script.
Copy your .json somewhere like the desktop and create directory path of \Data\F4SE\Plugins\F4EE\Presets\Plain PC.json, then pack \Data\ and it's sub-folders, now a mod manager knows where it needs to place the file and users who manually install can extract straight to \steamapps\common\Fallout 4\ . If you need to place files to other directories in \Fallout 4\ then create their respective directory paths also and pack to same archive. =)
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Copy your .json somewhere like the desktop and create directory path of \Data\F4SE\Plugins\F4EE\Presets\Plain PC.json, then pack \Data\ and it's sub-folders, now a mod manager knows where it needs to place the file and users who manually install can extract straight to \steamapps\common\Fallout 4\ . If you need to place files to other directories in \Fallout 4\ then create their respective directory paths also and pack to same archive. =)