I had the same issue with my '98 M-3. I don't know if you have the same hk system, but the principle is the same as long as you have a rear mounted amp.
I do know a good deal about audio, and could tell that the HK speakers up front were decent, as is the head unit and the disc player. What is lacking is proper equalization (the high end is really rolled off even though there are separate super tweeter) and ofcourse, it needs more low end than the two 5.5 kick panel woofers can produce.
The easy and best sounding for the money is what I did, in my opinion.
I got the wiring diagram for the trunk amp off of the web. I went to ebay and bought a two channel audio control equalizer for about $125, a pair of JL audio 8" sub woofers-$125, an active crossover- $50 and another two channel amp for $135 to power subs and saved a bunch of time and effort by not attempting to cut subs into the rear panel by making my own custom enclosures out of home depo supplied 10" tubes used for cement forms-$5 w/plywood discs cut a bit bigger than the tube used to seal each end w/the sub opening cut and mounted into one end. Each sub enclosure is behind a seat on the floor, can easily be disconnected to go in truck if I have passengers or fears of theft. The tubes were stuffed w/polyfiber and sprayed w/undercoating to dampen, then covered w/grey matching carpet from Parts express or jc witney.
You go in trunk, expose the oem amp and splice in the eq to the front channels, then xover to the sub amp and woofers. By crossing over at about 90hz, you essentially boost the power to the main front speakers by a ton since most of their power goes to driving the woofers. Once it's properly eq'd, the boost to the high end and proper sub eq gives you 95% of what you'd have by purchasing all new spkers, amps and head. All done for way less than $500, and can play louder than you need, unless you are one of those assholes playing their 15" subwoofers at 110db's so the neighborhood can hear their bad taste in music. But I digress.
Run the rears as they are, I use the spacial button to leave them as a good surround but just barely audible. They aren't worth eq'ing in my opinion. You could have a circuit city install doing what I suggested and still come in under budget.
For what it's worth, 90% of home systems just need eq and a subwoofer to sound like what you would pay 3x more for.