Are you using the crossover in the sub? Does your preamp have a crossover built in? If you are running full range to your speakers and full range to the sub, you will get some overlap with a crossover at 50hz. Remember that most crossovers are not 1st order, so you will get a gradual roll-off over a 12db to 18db range. The only way to avoid this is to have the system crossed over between the pre and power amps or between the amp and the speakers so the sub won't get too much of the same signal.
Some very high end subs will allow you to adjust for a good blend.
Some very high end subs will allow you to adjust for a good blend.