I added a JL XD300/1v2 + JL 8w3 to my 2008 S4 Avant back in the day. I originally spliced into the speaker level inputs going to the factory subwoofer, which I had disconnected. I found the quality to be very poor, taking the amplified signal from the factory monoblock amp.
I switched it out to use the pre-amplified signal feeding into the factory amp, which is also speaker level. This was what I ended up settling on. Tossed the amplifier in with the spare wheel well, grounded to the same. It was a very good upgrade, incredible bang for the buck. Here are some photos I had saved from 2014. Don't take the signal after amplification from your stock amp. You want to delete that thing from the equation.
A bit of a hack job by myself, but mostly clean when covers are all on. I loved that car.