How to create per subsite template file with custom press


I've installed Custom Press and I'd like to create template files for custom posts, for specific subsites. As described here I should be able to create template files but it seems it only works at network-level.
How can I create template files at site-level? How does it work precisely? Should I delete the loader.php line 13 and then I'll be able to create templates..? Where will these templates be saved in my files (FTP)?
See I don't want to share specific custom posts and templates within my whole network multisite.
Thank you very much for your help