The way that uploads work is that the files are immediately stored in a tmp directory on the server. It is up to you to then move them to somewhere useful - that can be outside of the htdocs directories if you wish.
A prerequisite for doing any file uploading work is to spend a good amount of time studying the various parts of the manual - which I find is one of the best written subjects.
It might be a pain - but uploading files is chock full of gotchas - there is no shortcut to reading the manual on this particular subject.
See especially the "Common pitfalls" section.