Can I set up two directories?

That wouldn’t work. The plugin creates a custom post type called “member”, and you can’t have another plugin trying to create the same post type again. You would have to do a lot more code changes to set up a second custom post type.

I think the better way to go would be to implement the “location” feature, and use the shortcode argument to display the directory for each location on a different page. Create 2 “locations” and assign the members accordingly. Then, use some other plugin that restricts access to certain pages, and set that up to make one of the pages for logged in users only.