So this may be a dumb question...
But can I ask what you mean by "marked up and added to the song library"?
Are these songs that will somehow aid in sequencing, or just a general listing/directory of songs that can be sequenced to?
Not a dumb question. I have marke dthe musical phrases of these songs. These are the places where you likely would want to change a animation effect.
The process is to go to the 4th tab over on the menu bar in Nutcracker. This is labeled "Projects". You then
select
1) Manager project
2) Add project
Now there is a pull down of songs that already have their music phrases marked. We are up to 9 songs now.
3) select a song
4) Select a target model (like your megatree or matrix)
5) select grame timing. i use 100ms
6) Now it save it. You can now edit the project.
7) You now see all of the music phrases of your song. There is a pull down that lest you pcik any of teh effects in your effect library. This in effect attaches an effect to that music phrase.

be SURE to now click save effects.
9) Select the sequencer you want (LOR, LSP, HLS, Vixen).
10) Select "Output project"
Now the project logic will go and calculate exactly how long your effect should be to fill in each phrase. It will then call each effect and build it. Finally it stitches all of the effects in yoru song (typically 20 to 30) and produces one output file.