Rule #1
Code which only applies to a page template should go in that page template.
Rule #2
Use meaningful file naming, eg page-gallery.php is more meaningful than page-custom.php
Rule #3
Include genesis(); at end of file.
Rule #4
Use remove_action to modify the loop
Rule #5
Avoid writing your own loop code – use genesis_custom_loop and modify output with remove/add actions. If you need a loop counter, one is already built-in to genesis_custom_loop