Hello Andy,
I don't know whether this is going to throw a spanner in the works, but the reason I asked if you had roof rails fitted was that I too got all enthusiastic about fitting roof rails and bars on our 2006 A3 Sportback.
That was until I realised that fitting roof rails (if not already fitted) entailed drilling the roof! - well at least on the 2006 model year. It would be wise to check if yours has any built in anchor points front and rear for the longitudinal roof rails to which the Thule cross bars will attach. If not, decide whether you are prepared to hand the responsibility of (correctly- first time?) drilling holes in your roof.
Probably well worth doing some homework before thinking about the roof bars. Of course, the quality and fitting of the roof rails become of paramount importance.
Let's hope your model year is different, and that it has built-in securing points for the rails.
It would be great if you could update us - do doubt useful information for other.
Kind regards,
Gareth.
p.s. I recall there were some aftermarket rails which 'hooked' under the top of the door shuts, but I decided against this.