Installation upload - not accepting folders?

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Hi all, 

I'm a complete newbie and am trying to work my way through the installation process.

While I am trying to upload the contents of the /upload folder, it won't upload the folders inside the folder?

So I've gone through to upload all of the files insides the folders individually but I am still not sure if this is correct? Do they need to be uploaded in their folders? Am I uploading EVERYTHING in the upload folder? 

And also, in every folder there is index.html - won't let me upload more than one of this file or it will override? Do I need to upload this?

Can someone please tell me -

Am I uploading every single folder under the upload file?
What about when there are multiples of the same file name and it won't let me upload both - ie admincp.js, announcements.php
module_meta.php
and do I need to upload the folders under upload as folders?

I am uploading them under public_html in my cpanel file manager hosting. 

Thank you in advance for anyone who is able to assist.