I've got a Audi A3 1.6se , ( Bose sound system installed )
Firstly do you have a bose amp and bass box all in one unit stored in the boot left compartment ( passenger side ) , black in colour designed with a arch to fitt over the wheel arch with a 6" sub in front and a round nokia sticker near that...
That box is the amp and sub powering the back speakers located in the side panels back seats location and sub woofer ,
If you have that you have a nice system but not loud as we all hope and the stock hu doesn't do much but could do better if you fit a cd shuttle in the boot , wiring is already the for it if you have the bose sound system ( cable located behind the sub/amp box - round din type plug )
I installed a pioneer wma/mp3 cd head unit but only get the front working at the moment
what i had to do to get that far was get a wiring kit ( audi a3 wiring to pioneer kit ) plus side panels
to get the back speakers working you will have to do new wires front the headunit to the speakers ( i haven't done that one yet )
Good luck , hope that helped