Can I create other folder to upload content to my website? I used to upload to only root level directory. I am thinking plenty of pages in root level directory result in more page load time for my website.
You can upload files to any directory of your website you have access to.
Or, to be more exact, your average file upload script creates a temporary copy of the uploaded file in the PHP temp folder on the server.
From there you can copy it to any location for which you have the appropriate permissions.
If you want to see a few examples, try Google: http://www.google.com/search?q=PHP+uploader+script
P.S. You posted this in the (X)HTML forum. You need to do something like this using a server-side language.
The number of pages in your root will not affect page load time.
Another thing, if you want to make that file private and don't want search engines to crawl it then you should consider adding a command to your robots.txt file. Just search 'how to prevent search engines from indexing a folder'. Hope that helps.
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