DO NOT alter any file that is a part of Drupal Core. Any file that is a part of Drupal Core is subject to being overwritten without notice. There are many ways around doing this, please jim [at] geekgene [dot] com if you need assistance.
Any module added to Drupal, be it a module downloaded from the Drupal web site, or developed internally, should go in its own folder within the /contributed/ folder. Drupal will automatically descend the tree and find the modules.
example: /modules/contributed/mymodule/mymodule.module
Do not place any module directly in the /modules folder. Any add-on module that does not reside in the /contributed/ folder is likely to be deleted when performing site upgrades.
Modules should be self-installing. Modules should include a .mysql file for creating any database tables at install-time, and should also include an .install file to perform the module setup work. Refer to the Writing .install files article on the Drupal web site.
Same as modules. Use a /contributed directory in the /themes directory for any downloaded or custom-developed themes. Hard-coding paths (to images, scripts, etc.) in a PHPTemplate file or sytle sheet is strongly discouraged.