Open CompizConfig settings manager. In the left hand pane click "Effects", then in the right hand pane click "Window Decoration". The pane will change and you will see a box entitled "Command". Change the contents to "emerald --replace" (without the quotes), and make sure that "Enable Window Decoration" is checked on the right.
Emerald can be a bit flakey, so you may have to logout and login again to see the change.