You can use a convention
http://wiki.fluentnhibernate.org/Conventions
*UPDATED
public static class PrivatePropertyHelper
    {
        // from http://stackoverflow.com/questions/1565734/is-it-possible-to-set-private-property-via-reflection
        public static T GetPrivatePropertyValue<T>(this object obj, string propName)
        {
            if (obj == null) throw new ArgumentNullException("obj");
            PropertyInfo pi = obj.GetType().GetProperty(propName, BindingFlags.Public | BindingFlags.NonPublic | BindingFlags.Instance);
            if (pi == null) throw new ArgumentOutOfRangeException("propName", string.Format("Property {0} was not found in Type {1}", propName, obj.GetType().FullName));
            return (T)pi.GetValue(obj, null);
        }
    }
public class CustomTableNameConvention : IClassConvention
{
    // Use this to set schema to specific value
    public void Apply(FluentNHibernate.Conventions.Instances.IClassInstance instance)
    {
        instance.Schema("My_NEw_Schema");
        instance.Table(instance.EntityType.Name.CamelToUnderscoreLower());
    }
    // Use this to alter the existing schema value.
    // note that Schema is a private property and you need reflection to get it
    public void Apply(FluentNHibernate.Conventions.Instances.IClassInstance instance)
    {          
        instance.Schema(instance.GetPrivatePropertyValue<string>("Schema").Replace(".", "_"));
        instance.Table(instance.EntityType.Name.CamelToUnderscoreLower());
    }
}
You must use only one of he Apply methods.
*UPDATE 2
I don't know I would recommend this but if you like to experiment this seems to work. Even more reflection :)
    public static void SetSchemaValue(this object obj, string schema)
    {
        var mapping_ref  = obj.GetType().GetField("mapping", BindingFlags.Instance | BindingFlags.IgnoreCase | BindingFlags.GetField | BindingFlags.NonPublic).GetValue(obj);
        var mapping = mapping_ref as ClassMapping;
        if (mapping != null)
        {
            mapping.Schema = schema;
        }
    }
    public void Apply(FluentNHibernate.Conventions.Instances.IClassInstance instance)
    {
        var schema = instance.GetPrivatePropertyValue<string>("Schema");
        if (schema == null)
        {
            instance.Schema("My_New_Schema");
        }
        else
        {
            instance.SetSchemaValue("My_New_Schema");
        }
    }