You'll need to do some manual mixing to make it work. My recommendation would be to use the following options:
In Output Format select: 1) 5.1 channels inside a 7.1 container, 2) JRSS mixing, 3) Check the box for "For Stereo Sources only mix to 2.1," and then 4) set subwoofer to "Silent"
That will do the following: mix all multichannel content to 5.1, and leave all stereo content alone. The subwoofer option just controls what the JRSS mixer will do, it doesn't affect the LFE channel on material that already has one, which means that 2 channel will stay 2 channel, but the .1 on 5.1 will still carry through.
Then, in parametric equalizer, add the following filters at the beginning of you filter bank:
1) Adjust volume for L and R; -3dB
2) Use mix channels to add SL to L and SR to R each with a -3dB adjustment
Then just do your routing normally overwriting whatever was in your SL and SR originally.
That should get you 3.1 with multichannel sources, and 2.0 with stereo sources. If you are concerned about losing that 3dB of dynamic range on stereo sources, you can also just setup separate zones for stereo and multichannel and use zoneswitch to route audio.
One issue you may run into is that it sounds like you may be using multiple subs and/or using your subs for more than just LFE? If that's the case you'll need to do some additional manual routing/levelling for non-LFE content that's going to the sub, but you may already have that sorted out in your existing setup? The main thing to remember is that LFE material needs to be 10dB louder than redirected bass from the mains/center. So you want to add any redirected bass to the LFE channel(s) with a -10dB gain. You may also need to reduce the volume of the LFE channel and any added bass by a few dB to avoid clipping (as shown for the surround mixing above).