Concerning the Joomla templates, there are 3 methods to define how a website has the access and depend the method used to create the slave site.
1) You can share the /templates directory and in this case you don't need to re-install the templates into the slave site. The templates become automatically available.
2) You can perform a full copy of the master website /templates directory and in this case, you may have the permission or not depending on the JMS templates / themes folers parrameter. It seems that you are in this case and that you don't have given the permission to install specific templates.
3) You can perform a partial share of the templates directory. In this case, you can share subdirectories present in the /templates.
All theses three cases are illustrated in the tutorial video 0.b slide 31-34.
www.jms2win.com/tutorial#jms12x-0b
To allow install your own templates into a slave site, you have to setup the "themes folder" parameter with {deploy_dir}/templates or {site_dir}/templates.
See also user manual
- Introduction + chapter 3.2 + chapter 3.3
See also the tutorial video CP-05
www.jms2win.com/tutorial#jms12x-CP-05
So in your case as you seems to have a copy of the /templates directory, it seems that you let the "themes folder" parameter empty. Perhaps you should put {deploy_dir}/templates to be able install new themes (templates) into this slave site.