It shouldn't be different from any other PHP application that uses
index.php for routing. Apache is smart enough to apply the
.htaccess that might be in subdirectories.
Nginx doesn't have an htaccess equivalent so usually the rules for both servers end up in the same file. If it doesn't work, it might be a simple matter of putting the
location block for the subdirectory above the other
location block so that priority is taken into account.