Based on the theme development documentation http://devdocs.magento.com/guides/v2.1/frontend-dev-guide/themes/theme-create.html here I could create a space for new theme in magento 2.0 but overriding the base template become more difficult to understand like altering page layout etc.
I am sure about you have just create magento 2 theme in your project.
So You have to just override templates into your custom theme folder from core module.
We have given here module-catalog template to override,
You can change as per your module override template file instead of
Just keep same manner in default module view folder file in above custom theme location.
please let me know if you have any issue