You can use DSP Studio > Parametric Equalizer to mute and cross-over lines.
However, if you have Klipsch computer speakers like the ones I'm familiar with, the subwoofer isn't on its own line. In other words, the Klipsch have 5.0 input and internally convert to 5.1.
If you're doing this for a critical listening environment, I'd recommend getting a multi-channel DAC instead of trying to link two DACs together. Zone linking is good for linking between rooms, but not good for linking where tiny amounts of drift could be disruptive.