Actually, the problem you have described is not "within Dreamhost" at all; it seems you just need help operating net2ftp.
There are several ways to get "into" the appropriate directory, which you should do before you upload the files. You can fill in the directory name in the text box in the upper left section of the screen (with the words "Directory Tree: root /" under it), or click on the little "directory tree" icon at the top of the page, next to that box and select a directory, or just click on the directory name in the list of directories in the content area of the net2ftp screen. Any of these will place you into the indicated directory.
Once there, you then upload your files, which will place them where you intend. Since it seems you have already loaded all the files into the "root" of your user space (instead of the "web root" or "base" directory of a website - a directory named like "yourdomain.tld") you could use the net2ftp "move" function (upper right section of the screen) to just move them to the appropriate directory without re-uploading them, but given the trouble you are having manipulating net2ftp, you may find that to be confusing.