Are you sure you put it into a seperate folder? You're supposed to uninstall all versions of RTW, re-install the gold version. Then go into your total war folder and copy all the folders (except BI) into a new folder of your decision which is clear. Then you extract the patch into that folder, and then EB, and so on. That's probably the error you're having.
I however, have done all this, and for some reason mine crashes mysteriosly with no error reports when it reaches the start screen. So far noone has really helped me so much. =P