Depending on which fine uploader methods you're using, you can pass custom headers via the customHeaders
property when you create an instance of the fine uploader. This answer has some potential guidance for you, but not knowing which methods you need the headers for means I can't be more specific: FineUploader - add authentication in header
Your first question is harder to answer, as it depends on how you're trying to use fine uploader and where you're sending your uploads. You could capture your files in a normal HTML file input, and then pass the files to the fine uploader when you submit the form, but that raises the question of why you would use the fine uploader in the first place.