Database migrations with Flask-Migrate involve changing your data models first, then generating a migration script using 'flask db migrate'. This script describes how to update the database schema. After reviewing the script, you apply the changes with 'flask db upgrade', which updates the actual database. This process keeps your database structure in sync with your application models. Skipping migration or upgrade steps can cause mismatches. The execution table shows each step and its result, while the variable tracker follows the model and database schema changes. Remember to always migrate after model changes and upgrade to apply them.