plugins or themes for network admins only

Hi,
I just purchased the membership, I believe this is one of the best investments I have ever made in online business.
Sorry back to my question.
I have certain plugins like SMTP settings that I need enabled only for the administrator or for that matter the ultimate branding theme for e.g.. Unfortunately enabling (network activate) it enables it for all member sites. After going over the videos and searching the docs it seems I could activate a plugin/theme on a persite basis but I am not sure whether we enable it for site id 1 or if its a network theme/plugin how to do that such that regular members do not have access to it.
What am I doing wrong?

thank you