Look in the file app/design/adminhtml/default/default/layout/sales.xml
, tracking.phtml is used several times. If this change is for a module then create a layout file 'yourmodule.xml' and enable it from your config file. Otherwise name it 'local.xml'. It's contents will have to be an update something like this:
<?xml version="1.0"?>
<layout>
<adminhtml_sales_order_shipment_new>
<reference name="shipment_tracking">
<action method="setTemplate">
<template>your/new/tracking.phtml</template>
</action>
</reference>
</adminhtml_sales_order_shipment_new>
</layout>
Also if you want to minimize number of copypasted layout statements you can use
<update handle="handle_name" />
inside different controller action handles. For example:
<my_handle_name>
<reference name="shipment_tracking">
<action method="setTemplate">
<template>your/new/tracking.phtml</template>
</action>
</reference>
</my_handle_name>
<adminhtml_sales_order_shipment_new>
<update handle="my_handle_name"/>
</adminhtml_sales_order_shipment_new>