When you create a new template you need to modify the "model" inside of the template for the phone type. For example if your doing a template for yealink t48's you would modify this:
<models>
<model ua="SIP-T46G">Yealink T46</model>
<model ua="SIP-T48G">Yealink T48</model>
</models>
to be something like
<models>
<model ua="SIP-T46G">Yealink T46 - custom1</model>
<model ua="SIP-T48G">Yealink T48 - custom1</model>
</models>
Then when you provision phones you will see your custom template with a different name. Name the actual file something that makes sense to you, then you can add/delete files as you need.