Just purchased one of the cheapo VAGCOM cables off Ebay.

Was googling where to find the ECU and how to use VAGCOM when I noticed someone mention about the aftermarket radio issue. I have an Alpine stereo in mine....am I going to need to disconnect it to use VAGCOM? I don't fancy blowing anything up in the process, The idea of getting VAGCOM was to save monies....

Also, where is the ECU in a vRS?

Then gotta sort out a laptop....the wife fried my one :/

The issue with aftermarket headunits and VAG mis-use of of the ISO connector don't affect VAG-COM.

The issue is very neatly detailed here

If you haven't disconnected the relevent wire, It probably means your headunit does use them.

There are several ecu's round the car for controlling the various sub-systems. For example engine ecu is under the wiper splash tray, airbag controller behind the central console, etc...

OK, so what happens if I do use it with the stereo plugged in? Just, its such a pain in the arse to fit all the cables behind stereo so want to avoid removing it :(

is it gonna fry anything or just not work?

Depends on your cheap ebay cable. The proper Ross-Tech cable makes allowances for aftermarket headunits and has a fuse fitted. Cheap chinese clones may well not, and could blow the USB/Serial port if you are not careful by placing 12V on a pin thats not designed for it.

It's all explained here:

The "Aftermarket Radio Problem"