How to place custom module template file in theme folder
Well you can place in the theme folder or you can leave it in the module. Drupal will look in both places. So if your implementation of hook_theme is a template, Drupal will look for the following files:


themes/bluemarine/custom.tpl.php
modules/custom/custom.tpl.php


If you read the documentation for hook_theme you'll get your answer for the question when you get to the path key:


  path: [...] Ordinarily the module or theme path will be used [...]