Thanks for the tips guys, though that didn't seem to fix my problem.
Maybe I was being too inaccurate.
I mean the arrangement position. When I fire a scene, then select the next scene and fire it while the previous one is still playing, the arrangement position doesn't go back to 1. 1. 1. but keeps on going instead. Is there a way to make it so that I wouldn't have to stop the whole thing before firing the next scene?
In regards to the click track, ditch the Live metrenome and build your own. I have done this on every daw I have ever used because I hate the sound of the click tracks frequency. Just create a new Drum Track (with drum instrument) and use suitable samples for the click and downbeat (a nice tight hi-hat for the click and a loose hat for the downbeat works well). Then create clips to suit your styles (4/4, 3/4 etc). Just play the clips when you need a click track or for your instance, create an arrangement and have it just stop when you need it too.
In regards to the Arrangement Vs Clips the arrangement will START when you press play and continue until you press STOP. The only thing that will affect it between pressing Start and Stop is the LOOP markers which can loop your arrangement.
AFAIK there is no way to use a clip to reset the arrangement playback to 1.1.1.
So what you are doing is using tracks in arrangement to play though but also triggering clips along with arrangement? If you need things to be starting and stopping etc I would just move your arrangement tracks into clips and create scenes. This would allow you to start/stop and do almost anything you need to. Using legato mode allows you to stop a clip and start it again without it starting from the start otherwise with it OFF triggering a clip will start it from 1.1.1 (just not arrangement).