aftermarket head unit on 2000 a6 avant but I still want to use audi subwoofer

I wouldn't bother doing anything if you're selling it. Buyers tend to be put off by aftermarket stereos.
If you have to do it then you need the RCA input adaper lead, this will plug into the rear RCA's on the Kenwood and feed the rear/sub amp. Autoleads part no. PC9-404
http://www.bluespot.co.uk/install/show_model.asp?id=17
or big Halfrauds stores carry them.
You will get a huge imbalance between the fronts and the rears as most aftermarket HU's have at least twice the power of the feeble Audi rear amp, so rewiring the rears is advisable. This will then leave you with just the sub, so use the above adapter to feed the sub out RCA's on the Kenwood to the rear amp. It will still be fairly quiet but at least you can then control it independently of the front/rear fader as the Kenwood should have a non fading sub control, so just whack that up to the max. Remember you need to connect the blue/white flying lead to the power antenna or remote on lead on the back of the Kenwood, you'll also need a fascia adapter and a power antenna adapter to feed the aerial amp.
The perm live & switche lives are wired the wrong way round on Audi ISO loom, so you'll need to swap them over to retain radio presets.