TL;DR / Executive Summary:
Are you looking for a quick way to understand best practices when upgrading your Zen Cart site? The easiest way to view it is as "a rebuild while keeping all the existing data."
This article contains 3 sections:
1. What an upgrade is, and what it is not.
2. An overview of how to rebuild a site using the new version, instead of upgrading.
3. How to upgrade while keeping the store live, and not losing any sales/customer/product