Hello markisbond,
I'll need some more time to check this out myself as I have not done this before. The Create Shortcut Method URL is an available action you put on a button click or focus event. In this case, it is most likely on the button that will email the customer (but before the actual action of sending the email.). The action will create an Action Result that will hold the URL. I believe you then save the result to a field on the table. Then on the email template you can use merge fields to put the field value onto the email.
Below is an example of a Create Short Method URL. It is a link to the Contacts portal. As mentioned in the Help Center article, I defined the activity RecordID from the current recordID. This is assuming the action is on the Activity screen. The Action Result is URLClickActivityCount and will have to be placed in a field on the table to be used in the email.
Note, it is only used for the four types of emails specified. Those are links to Method, the mobile login page, a portal login page or an email opt-out link. You can't setup a counter on any link you may have on your email. Say you have a link to your company's online store page. It will not count the times a customer clicked on the link.
Greg