Pixhawk architecture with simulink model?


At this moment I am using the Simulink Pixhawk support of Matlab. I have a question about the architecture of the Pixhawk. In the following Figure which I found on the website of Pixhawk, the whole architecture can be seen.

If I upload a Simulink model, which blocks in the Figure will be used? Are these blocks replaced or not used, or is the Simulink model using these blocks and the certain names?

Any help or advice would be much appreciated.