We almost always compose and deliver 2 or more cues. So the question here is how do you do it? There are two solutions as far as I know (though suggest others if you have done this differently).
1. One large WAV file with all the cues with spacing (no audio) between each cue for synchronization. The WAV must be put at the beginning of the film (i.e., 0h0m0s).
2. One WAV file for each cue along with instructions for each cue exactly where the file/cue/wav file starts.
Since I work often with filmmakers/directors who often have little to no experience with composers, multiple files for cues are too risky for a delivery option. I have even had one experience where the file was put starting at 0h0m30s and the film was released before I heard what they did. Needless to say that didn't sound very good :)
There is one 'issue' with option 1. If you deliver a soundtrack/wav file and the film is changed, for example, they add a scene or delete a scene. How do you want the modifications done to the soundtrack? For deletion, either you or the sound editor can delete the music (or empty space) for the deleted scene. For insertion, you need to add space and optionally write a cue and then resynchronize (possibly depending on how you do it) all the cues which follow (or at least the next one). For option 2, for deletion, you don't do anything, the sound editor merely deletes the cues/files you have for the deleted scene. For insertion, you deliver a new cue or cues and none of the other files are modified.
So I always (so far) go with option 1 - easy instructions (just create an audio track and add the file at 0h0m0s of that track), least likely to be error prone.
What has been your preferences and experiences?
This is valuable info! I've always sent my scores doing option 1 just to make sure everything was timed properly...but it makes complete sense to also include the individual cues for added flexibility.