How to upload script on the server?

Our scripts are designed so that they will only work properly if they are uploaded to the root directory of the server (domain). Here is how to structure should look like folders on the server after you upload our script.
1.) It shows two of our script, which have a different structure [2]. But note that they are installed in the root of the server (domain) [1]
upload script on the server upload script on the server
2.) Here in the pictures show how the script should not be installed (because it will not work correctly):
upload script on the server upload script on the server