While you have heard me say "don't modify Drupal core" a million times in meetings and email, there are times when it is just unavoidable to do something that is needed. If you follow the procedures, you will be able to keep your modified core modules in a place where they are easily identified for future reference. This also keeps your custom core hacks out of the way during Drupal core updates.

Cleanly overriding core modules in Drupal through the magic of multisite | Raincity Studios via Web Development Group