That is more or less correct -- both OJS and OCS employ a paper-tracking name-changing ID system that shows a revision number, stage ID, etc., so when a director uploads a version, it shows up as a director version and the file name "changes" to reflect that. It keeps track of all versions used in the system, and accordingly stores them under the appropriate Conference folder in /files.
If you wish to physically replace the original file, you can log in as Conference Manager, and click on the Files Browser link under General Management. Then you would use the Files Browser interface to navigate to the correct paper (every paper is given a submission number during the submission process; make sure you know the submission number of the paper you want to replace), and find the file you wish to replace.
The original author file would be saved in files/schedConfs/(conferencenumber)/papers/(submissionnumber)/submission/original, and would have a file name like 11-7-1-SM.txt. If you upload a file with the same file name as that on the server, the server version will be overwritten. Just be careful that you don't overwrite the wrong file by mistake.
You can also accomplish this via ftp, if you want.