If you want to rename a file uploaded thru a form, you will need to copy the temp uploaded file to the destination with the relevant name. The entire details are in the manual (upload file section). The only problem is that the owner of this file will be nobody and secondly the directory where you are copying to requires the requisite permissions.
The other option would be to ftp as a user first and then copy the file to the relevant directory.
If you have still have problems, kindly give the exact nature of the problem you are facing.
Nilesh