Working with a Drupal installation.
THE CONFIGURATION
settings.php holds the database credentials, in an array rather than as individual constants.
It also holds trusted host patterns, which Drupal warns about if unset.
THE UPDATE ROUTINE
Drupal requires the update script to be visited after any core or module update.
Skipping it leaves the database schema out of step with the code, producing errors that appear unrelated.
This is the single most common Drupal database problem.
CACHING
Drupal caches aggressively in database tables. Many apparent bugs are stale cache.
Clear the cache after any configuration change.
The cache tables can grow large and are safe to truncate, since they regenerate.
CONFIGURATION STORAGE
Modern Drupal stores configuration in the database and can export it to files.
That export is valuable: it lets configuration be version controlled and reapplied.
WATCHDOG
The logging table grows continuously if logging is verbose. Limit the retention in the logging settings.
WHAT NOT TO EDIT DIRECTLY
Drupal's structure is more interconnected than most. Prefer Drush or the interface over direct edits.