There’s an interface, Castle.Facilities.NHibernateIntegration.IConfigurationContributor, which gives one the opportunity to hook onto the NHibernate.Cfg.Configuration that the Facility will create, and add on the FluentNH mappings that you’d like (or do anything else you might like to enrich it, actually). You register your config contributor into your IoC container - the Facility will look for these during start-up (so, if you have more than one SessionFactory, you’ll need to filter on the ids). This ends up looking something like:

public class FooConfigurationContributor : IConfigurationContributor
{
  public void Process(string name, Configuration config)
  {
    if (name == "foo") // only enrich the session-factory configuration with id="foo" in the facility ioc-config.
    {
      var maps = from t in typeof (FooMap).Assembly.GetTypes()
                         where
                           t.BaseType.Name.Contains(typeof (ClassMap<>).Name)
                         select t;

      Fluently.Configure(config)
        .Mappings(x =>
        {
          foreach (var map in maps)
          {
            x.FluentMappings.Add(map);
          }
        })
        .BuildConfiguration();
    }
  }
}