The VAR SUB profiles are exactly what you are looking for! They eliminate the need for adjusting the crossover in the KD-S100 by making the mids and highs really vibrant. Just make a CD of each of the VAR SUB profiles and try each one to see which one fits with your front speakers best. Then adjust the volume of your subwoofer to match the front speakers.
Connect the subwoofer amp to the KD-S100 subwoofer output and you should be good to go with one of the VAR SUB profiles. The subwoofer output on the KD-S100 is not processed by Bongiovi DPS.