Here is what I did on my system. I WAS NOT HAPPY WITH THE BOSE UPGRADE I also wanted the best way to integrate an IPOD into the existing PCM system.
PCM incorporates the radio and CD whilst also controlling the audio and trip computer, it also controls the sports chrono functions, as well as it has separate control buttons for the rear spoiler, heated screen etc and also the controls for the climate control/air-conditioning. Based on all that there is no way to upgrade to a new head unit. So INTEGRATION is the way you have to go. Now there is a number of companies that are working on hacking the MOST bus. Hacking the MOST bus would allow you to hook the IPOD directly into the bus and in theory have the IPOD display on PCM. Then again there lots of controls on the MOST bus and I think you may have warranty and safety issues if you hack into it. So here is what the team who worked on my car did. We left the factory head unit in place as well as the factory amp. We first put in an Audio Control LC8 to take the speaker level output from the factor amp and turn them into line level outputs.
http://www.mobileaudiocontrol.com/ 
The dynamic range of this head unit is severely restricted to deal with the quality of the Upgraded but poor Bose speakers in the system and incorporate non-defeatable equalization curves aimed at correcting the response of those speakers, as well as protecting the relatively weak Bose upgraded speaker systems from overload. Examples of these include bass roll-off at increasing volume settings, or severe midrange EQ to tame the response of OEM speakers. Since we ended up replacing those speakers I needed to bring the full dynamic range back . To do this we now took the output from the Audio Control LC8 and we used a new unit from JLAudio called a cleansweep
http://www.jlaudio.com/press/CleanSweep05.html it returns the full dynamic range to any head unit and gives you a clean signal to put into your amplifier. This unit happens to have an auxiliary input.
We used this input to handle the IPOD. So now you have a full dynamic range output for both PCM and IPOD. To switch between PCM and the IPOD there are two knobs that we put in the cubby near the stick shift boot.
The first one is a volume control and push switch between the PCM and the IPOD. The second one controls the volume of the sub.
We then added an additional 5 channel amplifier from JLaudio in the bottom of the trunk area that gives you a 250 Watt Sub Channel plus a 100 watts a channel on the front two speakers and 25 watts a channel on the rear two speakers.
the sub box with 4 downward firing focal 6 in subs now has tons of base complete IPOD integration and sounds awesome.
If anyone wants to know more you can send me a private email.
But I don't want speakers like filing cabinets 
Sorry for going a bit off topic, here guys. 
