Is yours quattro or FWD
FWD models only really have brake upgrades for the front as the rear has stub axles but there may be some A6 parts that may fit.
if its quattro then you could go 345mm fronts with B6 S4 calipers which can be had on the cheap got mine for £180 posted, or used an S4 B5 320mm disc with the 2.0TFSI B6 calipers which is similar to the B6 S4's, as for rears you could go facelift S4 B5's 256mm but with those calipers you could use adaptors, custom hoses and B6 S4 300mm disc to give you 300mm rear with the S4 facelift calipers.
im going 345mm front and 300mm rears as it seems pretty cheaper than RS4 or brembo style upgrades