To upload files, you need to make sure you're in the subdirectory you want, then click upload files. Fill in the files you want, and click to upload them. If they have loaded successfully, you should see them listed below the subdirectory folder when that folder is active. I haven't had any problems doing this. I don't have any idea what might be wrong if the files aren't transferring properly....
If you think the files have been uploaded, you can try opening the url for the file you want, http://you.mu.nu/archives/subdirectory/file.ext, just to see if it's there....

Or use FTP - but you have to use active mode.

OK but how do I FTP?

Here's my problem. I know there are files sitting in http://simonworld.mu.nu/newdesign but I cannot seem to access them, even using File Manager. How do I get to them? I tried uploading a file to that directory via MT but I got an error saying I wasn't authorised...

I've tweaked the permissions, so try now.

Found the files...they were sitting in the public_html folder, so now I know where to upload to. Thanks for all the help.

I'm obviously going to have to download an additional FTP program. SmartFTP has only two options; passive mode and force port IP address.

Still getting this msg: A socket operation was attempted to an unreachable host.