Whenever you choose to use an existing template in a message you're writing you can choose to either link to the template or to clone the template.
If you choose to Clone the template you are choosing to not link the resulting statistics, like opens, replies, etc to the original. As such, your Reports will not reflect the accrued stats from the cloned template. Use this option if you do not want the results of this particular message used in your reporting for whatever reason, or if you want to alter the template and not have it affect the original and other templates linked to the original.
If you choose to Link the template then the stats accrued from using the linked template will pass on to the original, meaning your Reports will reflect them. In addition, changes you make to the linked template also make the same change to the original and all other linked templates.
Important: If you clone a sequence that contains Linked templates, the templates in the clone will also be linked. This means that when you make any changes to the templates in the clone, they will also change the template in the original sequence.