I really have zero experience with the stock system...
Now with that out of the way. It sounds like maybe the filtering is done after that harness, inside the amplifier/sub. Basically you will need to apply a low pass filter on your aftermarket amplifier to cut out those mid range frequencies and only allow the lower frequencies to pass through to the sub.
Another issue you may run into is setting the gain, basically you are starting off with a pretty weak signal. Some line out converters can boost this signal, but you should be able to counter it at the amplifier, just need to be cautions of clipping trying to amplify the weak signal.