You may need to convert the rig.
Usually if I want to customize a rig I will convert the character object so I can deal directly with the rig itself.
This doesn’t provide much in terms of flexibility, as you can’t easily adjust the rig after, but it does allow for easier customization.
In the case of the quad template I would set up the rig how you want it.
Bind it.
Then select the character object and hit “c”
The hierarchy is going to be kind of crazy, but look for a null named “Head_null”
Place your trunk rig as a child of this null.
You will then need to add these joints to the weight tag on your elephant mesh.
After you add the joints to the joint list you will need to assign weights to them.