The ShoqBox uses a database to store all file and playlist information.
However, it is not capable of creating this database it can only read it, thus necessitating a second program like MusicMatch or ShoqBox Buddy to update the database.

The database is an SQLite database which is an open source project.
You can download the source and binaries here.
Once you download the binaries you can easily query the database to discover it's structure.
Once you know it's structure it will be clear how to update the database.
Note: The format of the database that ShoqBox uses is version 2 not version 3 which is the latest version as of the writing of this document.
They are not backwards compatible so be sure to use sqlite.exe not sqlite3.exe.

When querying the database don't forget to escape any single quote characters (ASCII 96) that appear in file names.
Thus:
SELECT * FROM songTable WHERE cFileName = 'Beethoven's Symphony No. 9 (Scherzo)';CRLF
becomes:
SELECT * FROM songTable WHERE cFileName = 'Beethoven''s Symphony No. 9 (Scherzo)';CRLF
(Note the double '')

Another shortcoming of ShoqBox is that it does not deal with file names containing high bit characters.
i.e. ASCII characters greater than 127.
For this reason ShoqBox Buddy renames files to avoid these characters using the unaccented equivalent characters where ever possible.