How To Upload Image From Media Library Programmatically?
Not sure what you are trying to achieve here, but files uploaded via media are already permanent managed files once you get to the submit stage, I believe. 

The value in the form_state array you need is $fid = $form_state['values']['apply_now_image']['fid']);

You can then use that in a file_load: $file = file_load($fid);

So your code becomes 

$file = file_load($form_state['values']['apply_now_image']['fid']);
file_usage_add($file, 'user', 'user', $user-&gt;uid);
$apply_now_image_path = file_create_url($file-&gt;uri);
variable_set('rgit_apply_now_image', $apply_now_image_path);
variable_set('rgit_apply_now_image1', $file-&gt;fid);