The best way to do it is to put the Django admin templates inside your project. So your templates would be in templates/admin
while the stock Django admin templates would be in say template/django_admin
. Then, you can do something like the following:
templates/admin/change_form.html
{% extends 'django_admin/change_form.html' %}
Your stuff here
If you're worried about keeping the stock templates up to date, you can include them with svn externals or similar.