Hi @Joseph,
I had a look at your question and put together a short PDF that walks through the example, starting with the Hall sensors. It's attached (about 9 pages, with a few diagrams and links to the MathWorks pages I used).
Here is how it should help:
Hall sensors: it explains what the three sensors tell the controller. They give you six valid combinations, and each one means the rotor is in a particular 60-degree slice. There's a diagram showing the Hall signals next to the phase pattern they produce.
The Six Step Commutation block: it has the block's default table in plain form, showing which two phases get switched on for each Hall state, plus what the torque sign does, what happens with an invalid Hall value, and the custom commutation option. That table is the heart of six-step control, so it's a good place to start if you want to build your own.
Calibration: it explains why the Hall sequence has to be calibrated for your motor and what the calibration example is doing.
The rest of the model: it covers how speed is worked out from the Hall signals, open loop versus closed loop, and what each setup step in the example is for (ADC offset, encoder offset, host and target models).
Try it yourself: there's a short list of simulation experiments, like plotting the Hall signals against the gate signals in Data Inspector, that make the logic easier to see.
One caveat: I worked from the MathWorks documentation, not from the model file itself. I've marked in the PDF where I'm describing general six-step practice rather than something I confirmed in your model. If one particular block or subsystem is still unclear after reading it, tell us which one (a screenshot and your release number help) and I'll take a closer look.
Hope it helps, and good luck with the build!