Hi,
There is already some text added specifically in the order creation notification email for when a check payment is selected for that purpose:
echo '<p>' . JText::sprintf('PLEASE_SEND_CHECK',$amount).'<br/>'.$information.'<br/>'.JText::sprintf('INCLUDE_ORDER_NUMBER_TO_CHECK',$data->order_number) . '</p>';
That email is sent when the order is created, unless you deactivated it.
However, in the order notification email, that is sent when you click on the "email" button of the order edition page, there is not such text.
You would have to add something like that in the HTML version:
<?php if($data->cart->order_payment_method == 'check' ) echo 'My text'; ?>