Starting with version 2.2.0, Service Desk customers can be assigned to organizations during SSO.
This only applies to logins with a request-URL containing /servicedesk/customer, for which you can also enable am SSO redirection
in the redirection tab/ section of the plugin configuration ("Redirect SD Customer Portal").

Organization names can either be fixed in the configuration or read from a SAML response attribute.
If an organization does not exist, the assignment is skipped unless Add nonexisting Organizations is enabled.

Organizations created by the plugin will be assigned to all non-archived service desk projects.

You could later remove an organization from a project if you don't want it to be assigned to it or delete the organization completely.
All these actions can be found in the "Customers" section of each Service Desk project.

Please note, that organizations created with the add-on prior version 2.3.4 were not correctly assigned to the Service Desk projects.
You can fix this by manually adding the organization again to your Service Desk project(s).

You'll see that it is already available via autocomplete.
As soon as you did this, even the customers assigned to it with a version prior 2.3.4 will be visible in that organization again.