Out of order isn't as much a problem on cue lists as one may think. As long as you label stuff and are fast, the 'Go to' button is your best friend. I did a dance concert last year with about 500 cues, and it went in a different order each night. So I named each scene and programed in blocks. Like scene one was cues 10 thru 19 with 19 being the blackout, allowing me to record pre-load cues from 19.1-19.9. Worked well. It also gave each number a block of cues that lined up numerically cue wise and scene number wise.
For black outs on the fly, I use the Master fader or black out buttons. This way I can reset and pre-load the next 'scene' without anyone seeing what is going on, then just run the Master back up when we start again. For talking in between, I leave some lights on Independent and mark them with bright tape on the handle, so I can glance and quickly remember what is what for blackouts or light up in a blackout.