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I'm not sure what you meant by identifying "user", do you want to identify users by IP address? If a user enters his/her name on the form, then you can easily identify him.
The file uploads are organized per submission. Meaning it is attached on the submission for you to be able to see to what submission a file upload is associated to. You can check this guide on how to create file upload forms: https://www.jotform.com/help/332-How-to-create-upload-forms
I would also like to suggest that you create a form and test it in your end if it fits your actual needs. That would help you better to get familiarize with the form builder and how it works. You can register an account to us, it's "Free", have a paid subscription plan is optional.
Here's a sample file upload form that I created: https://form.jotform.com/61853798832976.
When someone fills it out, I will receive an email with a copy of that submission with the file upload. Just like this:
You can also find the submission data and the file upload on your account's submissions page. Here's how to look for it in your account: https://www.jotform.com/help/269-How-to-View-Form-Submissions
They are organized by submission so it's easy to see where the file uploads are placed.
I hope that helps.