As you have a full BOSE system, it's amplified front and back, so you will need the correct harness adapter, radio aerial adapter and facia adapter.
Autoleads parts are cheap and to be completely honest, due to the way the harness adapter works, you will hear a slight hiss at low volumes. For me it was unbearable, so I ended up replacing the whole OEM system, including the sub.
Parts needed (Part numbers are for Autoleads):
Audi A3 aerial adaptor - PC5-90
One-piece facia adaptor - FP18-00
Audi A3 fully-amplified adapter - PC9-408
To be honest, I wouldn't be surprised if you wanted to upgrade the rest of the system pretty soon as this approach doesn't do the new stereo justice.