re: But now, there is only one entry per organization and the organization appears multiple times… Is there anything that can be done about this?
In short, no, maybe, Connections does not create relationships between entries. It sounds to me like you’re trying to import individuals that are within a org/dept and not a list of organizations. Import your list as individuals with first and last names, do not make them contact names because that is completely different. Make sure each individual has their org and dept fields set too.
Now, go to the Connections : Settings admin page and click the advanced tab. Enable the link options for org and dept.
You’ll still be presented with a list of individuals but their org and dept names under their names will be links. When a user clicks on those links the results will be filtered by the org or dept the user clicked.
There’s a lot of assumptions I’m making … but, I hope it helps get you closer to what you’re trying to achieve.