There are several techniques to combat this problem. The primary method is to have a preamplifier between your computer and your amplifier. That way you always have hardware volume control.
You can also use a different audio device for JRiver MC than for your other stuff. Like your "really good DAC" for MC and built in audio for your other players, web browsers, etc.
I also recommend turning system sounds to off, or very, very low levels, otherwise you get loud sound effects sometimes (system alerts, etc). I also direct system sounds to a different sound device than I'm using with MC.
Finally, you could just use System Volume, in MC, but that's going to compromise sound quality in some way. Whether or not you can hear it or it is important is for you to determine.
Brian.