Is the agenda track actually mentioned in the GM tool kit at all?

Is there any advce on how and when to move the tracking token?

There is some advice on moving the stability token, and the idea behind the agenda track is relatively obvious but I would have thought it would be mentioned somewhere. I have missed something obvious and just can't see it for looking?

I've read it through couple of times and missed it also. I'm quite sure it isn't in there.

You didn't miss it. Not sure if that got cut for space reasons during layout or if they just felt that the Agenda track's use was self-evident, but it's not addressed.