I recommend you rename the root folder to 'geonames-tailored' and include that in your project and modify/hack it as needed. Yes, there are drawbacks to this approach and one could have a lengthy discussion about it but there are benefits, and it's just my suggestion to you based on personal experience; so your directory layout might end up:
/example.com/
/example.com/source-assets/ -> images/psd/etc
/example.com/src/
...
/example.com/src/geonames-tailored/ -> tailored and modified version
/example.com/src/geonames-tailored/geonames
...
/example.com/src/django-project -> your site's code
/example.com/virtualenv/
If you do wish to keep this as a separate app you can create a 'geonames_ext' app inside your django project and extend the code base through subclassing, monkey-patching, etc. - your directory layout might be:
/example.com/
/example.com/source-assets/ -> images/psd/etc
/example.com/src/
...
/example.com/src/django-project
/example.com/src/django-project/home
/example.com/src/django-project/geonames_ext/ -> your app modification code here
...
/example.com/src/django-project/contactus/home
...
/example.com/virtualenv/