Repetitive data that changes over time (lab members, news) is stored in _data/*.md. If you need to add or modify a job category, those are kept in jobtypes.md.
Papers go in papers/_posts/ and must have a name in the format YYYY-MM-DD-description. The description can be any text, but if it's absent the paper won't show up. There is a template in the _posts directory (template.md) that can be copied when creating a new paper from scratch.
Other pages are typically in a directory with the same name, e.g. the "Join us!" page is in join/join.md. You usually should not need to modify HTML files anywhere, just the Markdown.
The links in the navigation bar at the top of each page are defined in _includes/themes/lab/default.html.
Homepage carousel images go in /assets/images/gallery. Member photos go in /assets/images/members.
PDFs for publications go in /assets/pdfs. Be careful when adding PDFs from a publisher that names all PDFs the same thing.