However, considering your first post, you say you are uploading the files. I assumed that means uploading them to your wiki? (and thus internal links) Because I'd have to say that if you are using DokuWiki to to create a site whose content based on documentation and you are having that documentation not uploaded to DokuWiki but to an external server, you are doin' it wrong.
Don't quite follow the syntax here. But what's right is what works, not what exists in the realm of Platonic Ideas. My users can very comfortably download tgz files via external urls, files that have not been uploaded by means of the media manager but by means of sftp. When you are uploading files that are to be treated as internal media, then you should use the media manager. (Actually, I don't use the media manager, I use fckgLite and its file browser.)