Change the order of templates passed to twig

I found that when using multiple themes the order of the template locations passed twig would cause loading of the default them even if I'd specified an alternate theme.
'''$this->twiggy->theme('homepage')->display('welcome');'''
'''Unable to find template "_layouts/index.html.twig" (looked into: application/themes/default, application/themes/default, application/themes/homepage).'''