Are you talking about the test frequency for setting the gain. Or, the crossover frecuency setting?
For the gain: A 50hz test tone is good for setting the sub amp and a 1500 hz tone is usually good for setting the high end.
For the X-over: It really comes down to what sounds good to you. Personally, I don't like the higher bass. So, I usually set mine around 50 - 60hz.