Hi guys,
I believe the "stray bar" you have pictured there is the Blizz default extra bar. If you were using the default Blizz extra bars before installing Taeo UI and you chose to keep your old WTF folder then they will still appear. Just disable the bar(s) from the Blizz Interface options menu like normal.
As for what you should do with the WTF folder, the way Taeo UI works you don't have to delete it before installing. There is a minor chance of conflicts such as this but I believe it's worth the convenience for people who want to keep their old AddOn settings.
Lastly, the chat frames are an odd one. Blizz's API doesn't provide a good way to unlock and move those around. Taeo UI will attempt to place them correctly for you but you have to manually unlock them and then perform an update from the Taeo UI menu. Chat frames can be unlocked by right clicking on the tab - it will be the top option.