From a music theory perspective, this is about voice leading. You need to work with a set of rules to get you from one chord to the next by making decisions with each "voice".
Taking the example of CM7 and Gm:
Let's assume your CM7 has 4 voices and is in closed, root position starting from C3.
This means you have C3, E3, G3, B3.
Now, how do you want to move to Gm?
Gm could be any combination of G, Bb and D on the keyboard.
Furthermore, you have 4 voices in the first chord, so for part consistency you should be doubling one of the notes in Gm.
Generally, part writing is about finding smooth connections between chords (though this is not by any means the *only* way to write/compose),
and in doing such the objective is often to find the nearest notes for each part-
This would yield voicing such as:
D3, G3, Bb3, D4
Bb2, D3, G3, Bb3
If you want root position CM7 to go to Gm root closed position, still have choices- up or down?
You could have:
G2, Bb2, D2, G3
G3, Bb3, D3, G4
You would have to figure out what choices/decisions are built into your software about the note movements and what options the user has to effect the way the notes are transformed.
I don't think there is a fast answer that I can give that would solve this easily, as it is a matter of taste and you would have to spend a bit of time trying different rules and applying them to chord transformations to hear if they are satisfactory in results. The rules can make a difference as to whether you want Mozart or Stravinsky to come out the other end.
At the least, I would say try to make sure each note of your chord is represented.