Unless you are VERY electrically gifted, and trust yourself 100%, this is a job for a car audio professional.
To directly answer your questions, yes you can run heavier wire into the doors, but there is no need to. The stock German wiring is good. As to wiring the head unit to your amps in the trunk, you will need RCAs from the HU to the amps, and then need to tie into the factory speaker wiring from the old factory amp to power the speakers. You will need to tie into the harness at the HU for power, dimming, and antenna pickup. If you are installing a GPS Nav, you will also need to tie into the speed sensor wiring to speedo pickup.
If you research, you may find a plug and play adapter, but this isn't a common install like a Honda Civic so I doubt you'll have much luck there. I would have a good audio shop do the work.
Patrick
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