We may need a little more info about your setup, but I also run bi-amped speakers with JRiver so I can help from firsthand experience.
A few thoughts to get started: the key to the downmixing settings is that you'll need to use one of the "x channel in a y channel container" settings. In those settings the "x" is the mixing target, the "y" is the total number of channels available for mixing and routing. So, for example if you had a pair of 4-way quad-amped mains, you'd want "2 channel in a 7.1 channel container"; a stereo mixing target, but 8 channels available for mixing and routing. The only "catch" to be aware of is that the 2.1 setting is actually "2.1 in a 5.1 channel container" for compatibility reasons, but isn't labeled that way.
In your case you probably want to use 2 channel in a 5.1 channel container (just to have enough channels to do any routing work). Then you'd want to go to the first PEQ module, select the "mix channels" filter and use the "copy" function to copy Left to Surround Left. Then do the same to copy Right to Surround Right. I use Left and Right for my High Frequency and SL and SR for my low frequency, but it doesn't really matter as long as you know which are which. Then apply your crossover filters (high pass and low pass are appropriately labelled in the PEQ module) to the appropriate channels; you can select the order, the setpoint and which channels the filter applies to once you've selected the filter. Then you can add any necessary delay or other EQ. In this example your Center and Sub channels will be blank, or, if you have a sub, you can use them for sub mixing.
Does that make sense? If you need more info, please do ask; getting a bi-amped setup going can be challenging, but JRiver has everything you need from the software side and it's well worth the effort!