Options in the head unit are selectable by changing the configuration via a diagnostics cable, e.g. VCDS
http://wiki.ross-tech.com/wiki/index.php/Audi_Radio_Generation_II
The BOSE amplifier connects to the 4 line outs on the head unit (front and rear left and right). It produces the sub woofer signal from this to drive 5 channels. The head unit needs to be told that it is connected to the BOSE amplifier as otherwise it applies a sound equalisation profile that matches the car acoustics for directly driving the speakers / rear amplifier. This isn't required for BOSE as the amplifier does this itself so it would sound wrong. You also need to turn on the word "BOSE" so it appears at switch on!
You need a "CD Changer emulator" such as the Connects 2 or Xcarlink mentioned above for line in. These come in different types supporting USB, memory card and bluetooth streaming. Don't buy one of the cheap cables that is just a 3.5mm jack plug with the radio connector at the other end of a piece of wire, this won't work.