One thing you can do is to open all the file as a "project" in Smultron or TextMate or your favorite text editor. In JEdit with LilypondTools you can use the plug-in "Project Viewer" so you can have easy access to any part of your ensemble or orchestra work. This is faster than have a very very big file where you have to scroll up and down a lot. You can have a file called "
global.ly" with the options common to all parts and other files with options common to a group of instruments, like percussion (globalPercussion.ly) or strings. That's what I'm doing now, but I didn't get to the parts making yet...