Unless I'm missing something, you're saying the subwoofer and speakers share the same audio signal. As in a L+R stereo output from the DAC goes into the sub, then the powered speakers plug into the L+R output of the sub? I'm sorry to say it but you're running 2 channels of audio when you need to be running 3 ie you need a sound card, dac or amplifier receiver capable of providing at least 2.1 channels of output. Sure you can manually adjust the volume on the back of the sub but to put is simply there is no easy way of controlling the subwoofer output from within JRiver without affecting the speakers when the sub and speakers share the SAME output. Also adjusting the subwoofer channel in room correction when you're running 2.0 channels does nothing as you effectively have the lfe/subwoofer channel within JRiver disabled.
If however you have an audio device that is capable of running a 2.1 channel output, then you really want the subwoofer running on a dedicated LFE channel. Then your room correction dsp options will start working properly. Speaking from experience I run a 2.1 channel system myself, i have my subwoofer set to full range and room correction deals with all the bass management, crossovers and bass redirection. Bass sounds 10x cleaner when the speakers and sub aren't trying to play the same frequency, not to mention the crossover in most subs is average at best.