I have started documenting a Python project using Sphinx. It is the first time I use it - I am used to tools which work with a JavaDoc-like syntax, and I have some doubts.
I am by no means an expert on Sphinx, but from reading the documentation it seems that you can include TOC trees in subdirectories. The TOC tree page also gives some information on paths within the tree; have you experimented with using paths in the tree?