In order to use the Signature in your email templates you have to setup your signature in the "User settings".
There are two ways to add your signatures to the Emails.
1. Without Merge Tag
Navigate to the 'User Settings' page, select the 'Email Signature' tag, and add your signatures in the text box. You can select the option "Automatically add signatures to all outgoing emails" and you don't have to use the Tag every time.
Signature tags that are already on templates will not be affected. Recipients will only see one email signature.
2. With Merge Tag
Once you have saved your Email signatures, you will have to turn off the option on the Top and will have to use "Signature of the Rep" tag at the bottom of every template you want to use it in.