We are using 1 JSM project with multiple customers. A customer is going to be able to create and view tickets for their organization in the portal. That's the power of having customers use that portal. If I create a ticket for them, I can assign the specific organization to that ticket.
I have some customers that work for multiple organizations, and with the Organization Dropdown in the portal, they can choose which organization they want to see based on their credentials.
It may help you to make some user accounts that you have access to, so you can reassure yourself that it's working that way.
Hope that helps.
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