Hi,
If all your sites are in one site collection you can buy one site collection license.
You should be able to crate the SPJS library in the root of your site collection and use it in all subsites. If you had already installed it to your list when you had the SPJS folder directly in the subsite you need to remove this library from your site and then reinstall DFFS on the list when you have moved the SPJS library to your site collection root.
Please note that your existing DFFS config will be preserved when you get it reinstalled because the configurations are stored in a list in each site and is not removed when you uninstall DFFS in a list.
Let me know if you still have trouble.
Best regards,
Alexander