The documentation in docs/user is a subset of the guides that are present on the developer website. It will some day be all the guides, but we're doing this piece by piece.
To update the documentation, edit the appropriate Markdown file. For https://developer.android.com/ndk/guides/StandaloneToolchain.html, edit docs/user/StandaloneToolchain.md. The page layout is handled by docs/user/dac_template.jd, but that should not be altered unless the layout of DAC is changed.
The docs are not automatically pushed to the website. A Googler will need to run scripts/update_dac.py to publish changes. Googlers: simply run this script with the path to the root of your docs tree as the argument, make the commit, and upload the patch.