Where can I learn about how programs handle file systems like NTFS?

Question

I'm writing a program to handle the xbox 360's STFS files. I'm encountering all sorts of problems about how to keep track of used vs unused blocks, reading non-sequential files, etc. These aren't so much problems with the structure of STFS - it's just another file structure - but I don't know how I should do certain things.

I thought I would find a plethora of information on how file systems like NTFS and Fat32 are read by programs, but I'm only finding resources on how to work with the file systems using pre-made software and not so much how to make such software.

Here is a reference for STFS: http://free60.org/STFS