Maybe you could send me your preset.
If I have well understood: you're trying - within the same patch, i.e. in the context of one SINGLE - to manage 3 sound generator connected each to 1 output (I mean VCA here), 2 of them being "controlled" by the Sequencer and which should behaves as monophonic sound , the 3rd one being "controlled" by the keyboard and which should behaves as a polyphonic sound.
This is something which is not possible with Origin. A SINGLE preset can be monophonic or polyphonic but not both. What you build in the PATCH/RACK view is what you get in ONE voice. If the SINGLE is monophonic, 1 voice will be "created" (maybe more depending on the UNISON parameter) and *all* notes you play will be directed to this voice (or voices of the unison group). If the SINGLE is polyphonic, then several voices will be created when you play notes, each note being directed to one voice. So in your case, when you play a chord you "create" as much voices as there are notes in the chord. Therefore these voices will also generates the sound for the 2 outputs you want to be controlled by the sequencer, hence resulting in the "doubling" you mention.
To do what you want you'll have to build 2 SINGLES: one monophonic preset managing the 2 mono sounds, and a 2nd one - polyphonic - managing the 3rd sound. And then to regroup these 2 SINGLES in a MULTI preset. In the MULTI you can set the zones parameters to determine how these 2 presets will react to keyboard events.