What Damir said. All audio files are located in Stage Traxx 3. You can completely erase your iTunes library without having any impact on ST3. When migrating to a new iPad a migration assistant will allow you to transfer all apps & settings from an old iPad. This will also transfer Stage Traxx with all audio files to the new iPad. So nothing to do on this side.
Apart from that, just create regular full backups in Stage Traxx and copy them to your computer via iTunes filesharing. Then you can always restore your whole ST3 library even if your current iPad does no longer work at all.