This is a common question I get all the time: How do I put 2 (business) directories on the same WP installation?
Business Directory doesn't allow for a WPMU install (right now), nor can you install it twice on the same site to get that behavior. So what do you do?
One solution you might try is a subdomain/regular domain, both with WP installed, both with distinct copies of the Business Directory plugin, and both sites configured with the same content, but the URLs make the user look like they are on the same site. For example:
http://site.com -> directs to "main WP install"
http://site.com/page1 -> directs to "main WP install"
http://site.com/directory -> directs to "main WP install", "main Business Directory"
http://site.com/otherdirectory -> directs to "secondary WP install", "secondary Business Directory"
OR http://subdomain.site.com/directory -> directs to "secondary WP install", "secondary Business Directory"
This would require a bit of content duplication and some URL tweaks on both blogs so you make sure the users are on the correct site at any time (most of secondary WP site's links would go back to main WP site, one link on main site would go to secondary site (otherdirectory)…but that's probably the only way I know of, at this time...