Any time a customer uploads files (either from Custom Forms or Product Options) there is a record with a download link created. To access it, go to the System → Data → File uploads.
Example with the products options
Go to the product edit page
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
