I'm not sure I understand the basis of the question, but...
You can have all of the locos on both controllers, or you can have some on each, and some on both.
If you have locos on one controller that you do not want to be there, use the remove product option under tools to remove the locos you do not want from the HC.
Note: This will not affect the way the LMs are configured.
If the loco is not loaded on the HC it cannot be controlled from or consisted on that HC.