Your real issue will be finding an aftermarker amplifier small enough to fit in the location of the stock amp. If you do, you can reuse all your wiring except for your constant power and earth. I'd recommend running 4 or 8 guage wiring directly to your battery for power and a very short length of the same guage for your earth.
If you plan to use an aftermarket amp in a different location, ie. under the rear parcel shelf, you can pickup the remote turn on, front and rear channel ouputs for the h/u from the wiring harnes of your stock amp and then bridge them across to your new amp. You can then either run new speaker cable to each location or again run it into the wiring harness for the stock amp. Either way it will work fine...
Replacing all your stock speakers is a good idea. All the Bose stuff is 2-ohm, after market stuff is 4-ohm. It is quite easy to do. In the front doors you can fit 5.25" components. In the rear parcel shelf and rear doors you can get 6.5" drivers. You will also want to de-Bose your head unit. Again an easy thing to do, just find someone who has the VAGCOM plug and s.w.
Good luck, call out if you've got any further questions.