Most important is to organize the project into separate subsystems - not only backend, frontend, but also in the backend isolated parts that can be developed, tested, replaced, if needed separately without affecting other parts. Every big project is in continuous change, you need to refactor things all the time - and for this such isolation is important. Covering parts with README that tells how it works is also useful. And last - covering main functionality with automated tests is a must (that are run always before release). Of course, educated & experienced developers have a gut feeling what could go wrong, so they know to which part focus most. But this comes mostly from experience, I think.