OK, I think I understand what you are saying. You were placing the files in a directory that you had created within the web directory of your primary domain, not the automatically created one, up one level, in your home directory.
This is actually a fairly common error made by cPanel users coming to DreamHost, who are used to the cPanel method of having sub-domains as sub-directories within the parent domain's web directory, instead of the DreamHost way of treating domains and sub-domains as (mostly) independent and equal.
Don't worry, things are done a little differently here, but after a short while you'll become comfortable with it.
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