Here is the default behavior of the layout button explained in the documentation. To quote it, "If the number of displays are less than the number of ports, signals from additional ports appear on the last display."
In the newer scopes there does not seem to be way (in my understanding) to assign signals to particular axes. The way you can get around this is to use a mux block and feed in signals appropriately to make sure you get the layout and signals assigned reliably. Example snapshot of implementation and display below:
