So long as you click on the "show me how" thingy it activates. If you want to make sure, click on the advisor's mug to make it go away (it doesn't always bother after the script's been activated) and click on a settlement again - if the advisor prompt doesn't turn up, the script is active.

'Course, after you've played some two-three hundred turns without it I doubt if it'll do much good anymore.