To pause a cue you can click on the break button, on the side of the tempo tap button. But it will pause all your cues.
If you want to stop your first cue to start a new one,
You an click and hold the play button for more than 2 seconds, or click teh relase button then click the go button of the cuelist you want to stop.
Your you can set your 2 cuelist in the same bundle and this way when you start one cuelist the other one running stop automatically.