The recommended way to do File Upload is via this extension, which adds a bunch of features to the basic set provided in the ‘out-of-the-box’ File upload.
Salesforce makes a File Upload screen component available. It’s documented here. This component requires a recordId and associates the uploaded files with that record. It can accept multiple files and returns a collection of ids representing the uploaded file. These ID’s are of the type Content Document (Note that this is different from the older ‘Attachment’ Object Type).
More detail on the different ways files can be used in Flow is available here.
Automation Champion:Enhance Productivity by Uploading Files Directly from a Flow!)