Magento 1.9.1 – Responsive Transactional Emails: Totals Break Table

Use the google url builder get a good campaign url: https://support.google.com/analytics/answer/1033867?hl=en

It will take your base url and create a tracking url based on your info that you add and presents a link like: http://www.savethemage.com/?utm_source=Newsletter&utm_medium=Email&utm_content=Logo&utm_campaign=Order+Confirmation

Then take the part starting with ?: ?utm_source=Newsletter&utm_medium=Email&utm_content=Logo&utm_campaign=Order+Confirmation

and add it to the transaction email template for each link you want to track. Make sure you change the utm_content= to something unique for each link.

Then analytics will track all of those clicks.

The template is not aware of the email template that is calling it.
If your template needs to look differently based on the e-mail, you need to use 2 templates for 2 different emails.
I mean instead of using in both of them

 {{layout handle="some_handle_here"}}

in both of them, you need to use in the section one something like this:

 {{layout handle="some_other_handle_here"}}

and create the new layout handle in one of your layout files and use a different template file.