Create a new region within an existing one
You can use the region.tpl.php

And add a template_preprocess_region to add the new region variable with in this region. 

You can use the following code to add the region variable to the region.tpl.php

$variables['custom'] = block_get_blocks_by_region('custom');


So the over all process would be as follows. 

first you would create a preprocess_region function as given below

function theme_name_preprocess_region(&amp;$variables) {
  $variables['region_name'] = block_get_blocks_by_region('region_name');
}


next you would create a region template file called region--region_name.tpl.php

and print the variable $variables['region_name'];