Depends which adapter they used to integrate the new HU with the Audi loom that feeds the rears and sub. Usually it is the rears that are not loud enough.
First check the subwoofer in the boot to ascertain whether it is a Bose system or not as they are very different. If the sub has two 4" speakers then it's a Bose system, if it has a single 6" driver then it's non Bose. Not all 8L's had Bose grilles on the door cards.
The Bose system is fully amped so all the cabin speakers run off a separate amp in the drivers side cubbyhole in the boot. The sub runs off it's own amp inside the tupperware enclosure.
The non Bose system runs the fronts off the HU and the rears and sub off an amp inside the sub enclosure.
This is why the fronts are normally a lot louder running off an aftermarket HU which will have 2 x 50w going to the fronts with only 2 x 20w going to the rears from the puny Audi amp.
As you are getting different results front & rear then I imagine you do indeed have the non Bose system
There are 2 different adapters to feed the rear amp:
RCA input - which is a clean straight through wiring adapter taking the rear pre-outs from the HU and feeding them directly to the rear amp
Speaker input - this takes the high power speaker outputs from the HU and feeds them through a cheap hi-lo converter to take them back down to pre-out level which then feeds the rear amp.
I would guess they've used the latter and jacked up the level on it, but that's just a guess.
You really need to pull the HU out and post some pics of the wiring at the back.
The front woofers and tweeters both run off the same wiring so they couldn't be just driving the tweeters, although they could have quite easily blown the front woofers with the extra power leaving you with just the tweeters working - this sounds more likely, as the stock woofers are only rated for 2 x 20w
