This is from the PHP manual: http://www.php.net/manual/en/features.file-upload.php
Files will by default be stored in the server's default temporary directory, unless another location has been given with the upload_tmp_dir directive in php.ini. The server's default directory can be changed by setting the environment variable TMPDIR in the environment in which PHP runs. Setting it using putenv() from within a PHP script will not work. This environment variable can also be used to make sure that other operations are working on uploaded files, as well.
Also look at: http://www.php.net/manual/en/function.move-uploaded-file.php
This is a function in PHP since 3.0.16 and it moves an uploaded file to the location specified.
Finally if none of this helps check to make sure that your web server has the right permissions to write files to the directories that you are trying to access.