I have a hard time understanding what you are saying here. Let me try to decipher it:
I running RTW gold on vista. RTW is loaded on the users saved games folder for the purpose of EB.
Okay, you're using Vista and RTW Gold. When you say RTW is loaded, you mean installed? Why on earth would you install RTW in the savegame folder? Install RTW and EB somewhere else, such as c:\games\RTW_EB.

First attempt loaded, but the camapaign script couldnt be accessed on the advisor at the start of the game. its faded out.
I don't understand what you're saying here. If you did click "show me how", it should be successfully activated and the advisor should go away. What do you mean faded out?

I know that if this is not activated then essentiaaly the game fails as the triggers do not kick in.
Good.

Second attempt i now get three extra files to install as fugle warrior notes. Theyve been loaded into the main EB directory.
Which files?

However the short cuts are not working dueto the changes made in the target directory and hence i cannot now access anything .
Which changes in the "target directory"?