Ipstenu (Mika Epstein) on "WP Multsite with Separate DB's for each site"

You cannot simply modify wp-config.php to point at multiple databases

Yes you can. It's PHP.

Psudeocode follows:

IF domain == domain.com
  { db prefix = wp_foobar_ ; db name = domain.om_sql}

And on and on :) It's basic PHP if/then checks on the domain name.