i'm not sure if i got you right. you just wanna have an absolute path to the uploaded files, right?
if a file gets uploaded it goes to the default TEMP directory (if i remember right, you config that in the php.ini). you can read that config-entry by using get_cfg_var('upload_tmp_dir').
from there you move your file to it's final destination by using just copy() or move_uploaded_file().
maybe you should take a look at this. i found it quite useful.
http://www.php.net/manual/en/features.file-upload.php