What gear are we talking about?
Normally, it is best to use the line level subwoofer output on the receiver to go to the powered subwoofer, and hook up the speakers to the receiver. One then does as j_garcia says, and bypass the subwoofer's crossover if possible, but otherwise sets the subwoofer's crossover at its highest point. One then uses the subwoofer settings in the receiver, typically setting the main speakers to "small" and setting the crossover above the bass -3dB point of the main speakers. Thus, for example, with my system, my main speakers are rated 50-40kHz +/-3dB, so I set the crossover in my receiver at 80 Hz (as 80 Hz is above 50 Hz).