Having multiple organizations under a single Joomla instance is doable, but the problem comes from separation of moderation. You wouldn't want Organization A to be able to moderate Organization B, but that's not realistically possibly out of the box with CB since CB Moderator permissions are pretty globally encompassing and would likely require some custom work to try and implement limited organization moderation. If you, or your company, is going to handle moderation and the organizations just make requests to you then that could actually work out fine as then you'd be the sole moderators.
A single Joomla site using CB GroupJive for the organizations however could work very well. The organizations could either be categories or groups themselves, whichever you prefer. Then the organization would be admins or moderators of their organizations groups limiting their moderation scope. They can then invite people to join those groups, etc..
Group invites automatically accept during registration so that should take care of dealing with putting invited users into the correct organization.
Kyle (Krileon)
Community Builder Team Member
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