This one’s really easy. Make the cue buttons behave like they would in Ableton Live where only one track can be cued.
When you hit a deck’s cue button, the other cue, if turned on, turns off. Simple.
Now you have to hit both cue buttons every time, turn 1 on and turn the other off.
The “Auto Select” cue option does it for you, alternating between cued decks. Make the manual mode behave the same.