Shane,
Here is one possible way to approach this that I have used:
Use a standard template file that contains the structure for \header,\score, etc. To create a score, use this sructural template in one file (say File1) and \include a second file (say File2) that contains *only* the "music" (e.g., soprano = {}, alto = {}, etc. but no \score or other structural directives): \include "File2". You have to keep track of variables used in File2 so they are correct in File1. You compile File1 to get your midi/pdf output as you work on the score.This lets you create a set of File1s (File1a, File1b) for the various parts without building a score from the final book every time. To create the book, you use \book and \bookpart to create the structure and \include the set of second files, File2a, File2b, etc. but none of the File1a, File1b files. Your \book might look something like this (without all the braces):
\version blah
\language blah
\header blah
\include "File2a" [say, choir parts]
\include "File2b" [say wind quintet]
\book
\bookpart
[optional \header]
\score [uses all included music for a FullScore]
\bookpart
[optional \header]
\score [uses only wind quintet music to create score for them alone]
...
Make sense?
I use \book and \bookpart for nearly everything I do now because it lets me create a Title page, with lyrics (I mostly write choral music), but I've done some more complicated things that included instrumental parts, multiple scores (Full Score, Organ Part, etc.) all with \book and \bookpart. In case you haven't seen it in the documentation, one very valuable directive is " \bookOutputSuffix "Instrument-Parts" that tells LP to output a PDF file with the indicated suffix added to the filename. You can use one in each \bookpart. Brilliant.
Hope this helps some.
Regards,
Guy