another melt down…help please

I made a post a few hours ago asking how to get a wp theme loaded if it doesn’t come as a zip file but as about 15-20 files. Someone here advised/reminded me that I could upload the files with the FTP. This is what I did.
I opened ftp, and in the right side clicked on public html, then clicked on the addon domain name, clicked on wp content, then clicked on themes.The two standard issue theme names were visible.
On the left side box I first had the desk top, then clicked on the theme folder, it opened up and showed all the files. I selected all and dragged/dropped it to the right side.
A moment later I get a message saying there is already a file called index php, and what did I want to do? Overwrite it, write a new one etc etc. I told it to write a new one.(just a guess, I don’t know what I’m doing when things like this happen)
It went on and loaded all the theme files, and when I went back to the site to look, there is no new theme listed, just the two standard themes.

I opened up the ftp again, but now I instead of opening the desk top on the left box I have about 15 files I don’t recognize at all, and I can’t find a desktop icon anywhere in them. The right side box is just like it usually is. But the huge problem is that I can’t get the desktop to open for ftp.

What have I done, and how do I fix it? Even though I did this with just one addon domain, because the ftp now doesn’t see the desk top I can’t work on any other site? Help?
or do I just delete the addon and rebuild it from scratch?