Hi Mafisto,
Good news. As you've got the Bose system, then installing the Empeg is actually very simple. If you had the stock audio setup, then you would need to add an amp, and possibly replace speakers (depending on how you like the Audi supplied items).
There are three things that you need:
1) The removal keys for the Bose head unit (if you ask your Audi dealer nicely, they will probably remove it for you FOC).
2) An adapter loom to allow the ISO connector and the Empeg pre-amp outputs to interface to the Bose amp connector.
3) Facia adapters to make the opening on the TT standard DIN-E sized.
When I did the install in my TT, then you couldn't actually get an adapter designed specifically for the Bose system. From reading around, and from looking at the service manual for the TT, I was able to work out that the TT is almost identical to the A3 (with Bose). I therefore purchased the A3 adapter and modified it to suit. As I had the wiring diagrams for the TT, this was actually easy.
In the TT, the Bose system only has one set of L+R pre-amp inputs. All of the balancing of the speakers is actually performed by the Bose amplifier. This is most evident by the fact that you can't perform any front/rear fading in the Bose setup, but you can in the stock setup (at least on the TT Coupe). In the TT, the loom connector is configured with many more pins than it actually needs, as it comes from the A3/A4. If you look at the wiring diagram, there are two sets of pins for front and rear pre-amp inputs. On the TT with Bose, only the front pre-amp connectors are actually used.
The A3 loom adaptor is wired so that the pre-amp connectors are mapped to the rear pre-amp inputs on the connector. To make it work, you simply remove the pins on the adapter from the rear positions, move them to the front positions, and it just works. Fortunately, the Bose amp takes a 4v pre-amp input, so it matches the Empeg perfectly.
In the UK, a company called Autoleads can supply all of the parts that are required, but I don't know where you would get them in the US (Crutchfield, perhaps?).
I'm currently away from home, but when I get back, I will either post, or send you the pinouts for the Bose connector.
Alternatively, I do still have all of the bits for installing in the TT, as I no longer have mine. If you want them, then I'm sure we could work out a deal.
Hope this helps,
Andy.