I think you may be confused about how multi out works. To summarise the output channels are:
Channel 1 outputs the whole chord
Channel 2 outputs the bottom note of the chord
Channel 3 outputs the second note of the chord
Channel 4 outputs the third note of the chord.
So if you are playng the first inversion of C maj
Channel 1 outputs the whole chord (E,G,C)
Channel 2 outputs E
Channel 3 outputs G
Channel 4 outputs C.
Channel 2 should not output C because that is the root and you are using an inversion.
There is a short tutorial introducing Multi Out although it is based on Reaper.
If you want to retain the root in the bass whilst still using inversions this is not musically an inversion, it is a voicing. To achieve it try using voicings for your chords such as voicing 2, 4 or7. Alternatively you could add the bass on the CHORD page when you create the inversion of the original chord…
Hope this helps clarify Multi Out.