I heard back from my PreSonus contact, and he had this to say:
"I don't think he is asking a
Monitor Station question; he is asking how to set this up in Focusrite's Mix Control and in Cubase...The Monitor Station will let him connect up to three input audio streams (TRS1, TRS2, and Aux/Phono), allowing him to switch between and compare different inputs...He has his Saffire outs connected to Stereo In 1 (TRS1) on the Monitor Station and is sending his DAW returns there. No problem, he has that working...He wants to send a separate headphone monitor mix from his interface to a separate interface out to Stereo In 2 (TRS2) on the Monitor Station. So presumably this mix will be a custom mix of DAW returns plus the mic input, which he needs to create in Mix Control and send to the Monitor Station. Wiring to TRS2 should work fine...So now he can switch between TRS1 and TRS2. He also can sum the two mixes instead of toggling between them if he wants to but in this case he probably doesn't want to. (The Main/Cue Source buttons can be changed to best suit the studio environment. You can enter Input Sum or Input Toggle Mode by pressing and holding the ST1 or ST2 buttons respectively while powering on the Monitor Station.) But I bet he knows this. It sounds to me like his problem is before the Monitor Station, setting up the interface mixes in Cubase and Mix Control."
I realize that doesn't provide you with a solution per se, but I hope it clarifies the Monitor Station's role in your scenario. Perhaps if you routed your headphone mix from Cubase to outputs 3 & 4, you could route the DAW mix to 3 & 4 via an aux bus, and then you'd be able to toggle it in and out of your headphone mix, if need be.
Anyway, I hope that's all of some help to you. Good luck!