By default, https://apiary.io/ adds "Introduction" and "Reference" headings to API documentation. The headings are not visible in the built-in Editor and it does not seem to be possible to suppress them or to add more headings in the same style.
I'm familiar with Markdown and have learned the essentials of MSON but so far I have failed to find a solution.
(I work for Apiary)
The Introduction and Reference are the key groups of the Table of Contents (ToC) in Apiary API Documentation, and can't be changed.
The ToC is visible also at the Editor page as long as your browser window is wide enough (you can drag the divider between editor/preview to make the Preview larger).
The suggested way of the structure of your API Description Document (ADD) is to have one
# API Name, then multiple## Group ...with### Resource XYZ [/path/to/it]under those Group(s) = so you'll see the results in the ToC nicely rendered.