Hi Anders,
As a production manager who is often overseeing several designers and trying to integrate their Qlab shows together, I run into this problem a lot. My solution may or may not help with your situation, but it's a handy trick. I've found that the easiest way is not so much to integrate the separate cue lists, but to instead keep them separate and create one master cue list that references them to run the show. This is very handy when you have multiple designers who all need to revise their parts of the show - otherwise, each day, or each tech rehearsal, you're having to figure out how to get everyone's changes into the master show...
In your case, you would create one master cue list that cues your sounds and lights and sets their timing, etc. But this list consists only "go" cues that reference the other two cue lists. Audio and lights remain separate cue lists, and the people working on those separate parts can take them home, work on them individually and make any changes they need to, without affecting the master list (assuming their cue numbers remain the same). Obviously there are then some changes that can only be made through the master list, but those are only things having to do with timing and how the two lists interact (ie. making a sound cue go an extra 2 seconds after a light cue, etc), and I find that those changes are generally a lot less time consuming and can be done quickly, while letting the designers do the fussy work on their own time.
It's a simple trick, and like I said, may not be the answer you're looking for, but in my experience, the more complicated the show, the more time it seems to save everyone.
Cheers,
Stephen