Security Ninja connects to MainWP through an extension you install on your MainWP Dashboard site only. Child sites need Security Ninja itself. They do not need the MainWP addon.
Pick your path
Premium (recommended for Pro, Agency, and AppSumo)
Use the premium Security Ninja for MainWP zip from your account. Full setup, license activation, child sites, and sync:
Install Security Ninja with MainWP
Do not install the free wordpress.org plugin if you already have a premium license. The free build does not include premium code.
Free extension
If you only need the free addon from wordpress.org:
Install the free MainWP extension