Go to the System → Data → File uploads
Every time customer upload files there is a record with download link created. File upload field available in the Custom Forms and Product Options.
Example with the products options
Add new Option with the element type File
Set the allowed file extensions with a comma-separated list. Set the subfolder name in the /admin/system/uploads/ directory. It will be created automatically if not exist
Customer select the file and add proceed the order
Once order placed the file selected by customer saved to the directory you set in the options settings