How to maintain and update a Drupal installation and its modules? I'm looking for a comprehensive tutorial on best practices for updating and maintaining a Drupal installation and it's modules where there are multiple instances of the site, that is having a development instance and a live instance, and methodologies for updating the live site with changes made on the development site, and avoiding database conflicts.

TL;DR


Best practices for updating Drupal and it's modules to newer, more secure versions.
Best practices for mirroring changes made in a development instance of a site to the live instance of the site.


Note: I am using Mercurial to track changes.
I'm not sure about a guide but you will want to look into Features for change management between instances and Drush for updating Drupal and it's modules. 

Anything you can't do for the database in features should be placed in an install file and applied as updates to maintain the db between instances.