Two Remote Browser's Share Same Files!

I have to domain names that I use for vbulletin forums. Just recently purchased one and was going to upload and then install the files onto the new domain but the all the files and sub root folder was already in that remote browser on SmartFTP. Now I'm unable to install the files as I was planning to change the folder name to that of the sub root folder but can't because it will merge the files. How do I go about this and what do I do to fix? Thanks!

forgot to mention that I'm using the same server for both domains, does that matter?

Hello ..

I'm sorry but I don't understand your problem. You can always delete the files on the server first if you think that merging doesn't work as expected.