Re-install or workaround?

I have two blogs. One is up and running the other I am having problems with. They emerged when I tried to change the theme at dashdashdash.com. I went through the codex and help and am certain I did it correctly but I can’t call up the new themes in dashboard – presentation. Only the defaults appear.
I then looked at the server side of things and discovered my successful (ie working blog) has three folders at the top level; fefihohum.com, logs and Maildir plus 4 documents.
My unsuccessful blog dashdashdash.com starts with six folders(wp-includes,wp-images,wp-content, wp-admin, htdocs,cgi bin and a license text). I suspect the unsuccessful blog should mirror the successful one.
My question then is this; can I simply make a new folder within Fetch(my ftp vehicle) and name it dashdashdash.com and then transfer everything over, creating a new top level, or would I be better off doing a completely new re-install?
I don’t want to break anything.