The climate control on my vRS is so confusing to use and why do the little yellow lights not light up for certain positions is it something to do with the auto function or are they not working. Also do the little blue and red lights on the two temperature dials light as mine do not. Have looked in the owners manual as this states they do but cannot get mine to light up. 

By yellow lights I assume you mean on the fan speed control, these don't light up in "auto".  The Blue and red "lights" on the dials I think are just dots of colour to indicate it's a temp dial rather than actual lights, certainly mine have never lit up.

 

I think there's a VCDS change that can be made to show the fan speed in auto if it annoys you.

Not sure how it can be confusing, switch AC on, set it to Auto then set your desired temperature...... Not sure it can be made any simplier.....

In manual A/C mode, the fan speed led goes out when you reach the speed that the auto setting would be running the fan at (hope that makes sense).

If you can find someone with VCDS then you can fix that so that auto mode shows the fan speed setting, and I'm guessing this would fix the issue you are seeing.