The key points would be:
- Make sure your angles are the exact same length.
- Make sure they contain the same gop structure (Auto Scene Detect in Encoding is a big no-no)
I don't know in Scenarist whether you would 'break' the film down into pieces (which you can do with the 'start' and duration dialogues), and they join the pgc's together seamlessley, so that you have seperate chunks with the angles.
Obviously with Maestro you can have multiple bits of video on your timeline, whereas with Scenarist each 'track' comprises of one piece of audio, video etc.
ApolloOne may be of more use, depending what his 'weapon of choice' is.
DVD-BOY