You would probably want to set the Output Format DSP to 2.1. However, it looks like that only opens up 6 channels. For your situation it looks like 8 channels should be opened up and one will be unused. Maybe Matt can make a change that will allow 8 channels with 2.1. This is only necessary if you have a 5.1 or 7.1 source, but need it played back on a 2.1 system which is what you have.
If you have a stereo source you can set Output Format to 7.1, but set mixing to "No upmixing or downmixing." Now you will have 8 channels, but the original signal will go to channels 1 and 2. Now use the Parametric Equalizer and Mix Channels to copy your channels to the other channels. I would do the following steps.
Use the Room Correction DSP to create the crossover for the subwoofer by adding the crossover for the left and right channels. This will add info to channel 4 for the subwoofer.
Move Parametric Equalizer so it is after Room Correction. Use Mix Channels to make these changes:
Move Right to Surround Left
Copy Surround Left to Surround Right
Copy Surround Left to Rear Left
Copy Left to Right
Copy Left to Center
Now channels 1, 2, & 3 (L,R,C) have the left channel information and channels 5,6, & 7 (SL, SR, RL) have the right channel information. Channel 4 (Sub) will have the subwoofer information. You will connect channel 1 to the left channel woofer, channel 2 to the left channel mid, and channel 3 to the left channel tweeter. Do the same with 5-7 for the right channel. You will also have to use the gain setting for each mix channels so that the woofer, mid, and tweeter are all playing at the same level.
Now you can use REW to generate a convolution file which you can load into the Convolution DSP in JRiver. You can only load one file, so you may need a way to combine all files or else create a convolver text configuration file. I don't have any experience in this area.
If you would rather just create crossovers in JRiver you can do that easily enough. Still using Parametric Equalizer you can add high pass and low pass filters to each channel. If your woofer crosses to the mid at 800 Hz and the mid crosses to the tweeter at 3000 Hz you can a low pass filter to channels L and SL (woofers) at 800 Hz with whatever slope you want. Then add high pass filter to channels R and SR (mids) at 800 Hz and a low pass to channels R and SR (mids) at 3000 Hz. Finally, add a high pass at 3000 Hz to channels C & RL (tweeters).
You can use the new loopback feature in JRiver to measure with REW and adjust the crossover frequencies and slopes by using a close mic on one of the speakers. Once can also have REW generate some filters to smooth the response.
Once you get the crossovers adjusted how you want you can use REW to measure the room from the listening position and you can add more filters using Parametric Equalizer 2.