I created (cloned) a System Admin profile to enable Lighting Experience for it, and disable Lightning Experience for my other users but I don't have an option to disable? The checkbox is checked and can't be unchecked/edited.
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Magda, yeah, standard profiles aren't editable so you can't disable the Lightning Experience User permission in this case. You can do the opposite -- use the cloned custom profile to disable the user perm and assign users to the new custom profile. Then leave admins with the standard System Administrator profile so they'll get Lightning Experience access.
See if this help topic helps explain your options:
https://help.salesforce.com/articleView?id=lex_enable_users.htm.
