I believe you can do this a couple of ways. You could have one repository and create folders at the root of the repository for each client. You could then create a group for each client and put their users in that group and then assign that group access to only their client folder. I know that you can reference a specific repository using a search URL. I would imagine it would also work to log into a repository, but I'm not certain.

I also believe you could have multiple repositories and using the SDK create logins on a website that would allow the use to log into their repository only. I have not done this specifically, but have seem similar things done with applications.