You can overwrite a sites nginx config by putting a new one in /home/user-data/www/domain.conf
If the file does not exist, create it, add what you want (like overwriting document root, etc) and save, restart nginx (service nginx restart) and it should take affect. If it does not take affect you will need to run web update in the mailinabox git directory under your own user account.
An example of this is the old way of enabling PHP on sites ( Enable PHP on sites ) as you can see here.