mapping.References(x => x.SomeReference).SetAttribute("index", "IX_index");
mapping.Map(x => x.SomeField).SetAttribute("index", "IX_index");

create index IX_index on ApplicantProgramDatas (SomeField, SomeReferenceId)

create index IX_index on ApplicantProgramDatas (SomeReferenceId, SomeField)

<hibernate-mapping xmlns="urn:nhiernate-mapping-2.2">
  <database-object>
     <create>VALID SQL</create>
     <drop>VALID SQL</create>
  </database-object>
</hibernate-mapping>

namespace NHibernate.Mapping {
    public interface IAuxiliaryDatabaseObject : IRelationalModel {
        void AddDialectScope(string dialectName);
        bool AppliesToDialect(Dialect dialect);
        void SetParameterValues(IDictionary<string, string> parameters);
    }
    public interface IRelationalModel {
        string SqlCreateString(Dialect dialect, IMapping p, string defaultCatalog, string defaultSchema);
        string SqlDropString(Dialect dialect, string defaultCatalog, string defaultSchema);
    }
}

var sqlCreate = "CREATION SCRIPT";
var sqlDrop = "DROP SCRIPT";
cfg.AddAuxiliaryDatabaseObject(new SimpleAuxiliaryDatabaseObject(sqlCreate, sqlDrop));

foreach (var collection in Collections)
            visitor.Visit(collection);

        foreach (var property in Properties)
            visitor.Visit(property);

        foreach (var reference in References)
            visitor.Visit(reference);

using System;
using System.Collections.Generic;
using System.Diagnostics;
using System.Reflection;
using System.Text;
using FluentNHibernate.Cfg;
using FluentNHibernate.Cfg.Db;
using FluentNHibernate.Mapping;
using NHibernate.Cfg;
using NHibernate.Tool.hbm2ddl;

namespace FluentNHib
{

    public class Master
    {
        public int Id { get; set; }
    }

    public class Child
    {
        public int Id { get; set; }
        [MCIndex("A", 0)]
        public Master Master { get; set; }
        [MCIndex("A", 1)]
        public string Name { get; set; }
    }

    public class MCIndexAttribute : Attribute
    {
        public string indexName;
        public int indexOrder;

        public MCIndexAttribute(string indexName, int i)
        {
            this.indexName = indexName;
            this.indexOrder = i;
        }
    }

    public class MasterMap : ClassMap
    {
        public MasterMap()
        {
            Id(x => x.Id);
        }
    }

    public class ChildMap : ClassMap
    {
        public ChildMap()
        {
            Id(x => x.Id);
            References(x => x.Master).Index("A");
            Map(x => x.Name).Index("A");

        }
    }

    class MySchemaExport : SchemaExport
    {
        internal struct MCIndexField
        {
            internal int index;
            internal string Name;

        }

        internal class MCIndex
        {
            internal string IndexName;
            public readonly IList fields = new List();
            public string Table;

            public void AddField(string name, int indexOrder)
            {
                fields.Add(new MCIndexField {index = indexOrder, Name = name});
            }
        }

        private readonly Dictionary indexes = new Dictionary();

        MCIndex ByName(string name, string table)
        {
            MCIndex result;
            if (!indexes.TryGetValue(name, out result))
            {
                result = new MCIndex
                    {
                        IndexName = name
                    };
                indexes.Add(name, result);
            }
            return result;
        }

        public MySchemaExport(Configuration cfg) : base(cfg)
        {
            foreach (var type in typeof(ChildMap).Assembly.GetTypes())
            {
                foreach (var prop in type.GetProperties())
                {
                    var attr = prop.GetCustomAttributes(typeof (MCIndexAttribute), true);
                    if (attr.Length == 1)
                    {
                        var attribute = (MCIndexAttribute) attr[0];
                        ByName(attribute.indexName, type.Name).AddField(prop.Name, attribute.indexOrder);
                    }
                }
            }


            var createSqlProp = typeof(SchemaExport).GetField("createSQL", BindingFlags.NonPublic | BindingFlags.Instance);
            var wasSql = createSqlProp.GetValue(this);

            var sb = new StringBuilder();
            sb.AppendLine("");
            foreach (var mcIndex in indexes)
            {
                sb.AppendLine(string.Format("create index {0} on {1} ({2})", mcIndex.Value.IndexName, mcIndex.Value.Table, mcIndex.Value.fields));
            }
            createSqlProp.SetValue(this, wasSql + sb.ToString());
        }
    }

    class Program
    {

        private static void BuildSchema(Configuration config)
        {
            new MySchemaExport(config)
                .Create(s =>
                            {
                                Debug.WriteLine(s);
                            }, true);
        }

        const string fileName = "c:\temp\temp.fdb";

        private static string GetConnectionString()
        {
            const string userName = "sysdba";
            const string password = "masterkey";
            return String.Format("ServerType=1;User={0};Password={1};Dialect=3;Database={2}", userName, password, fileName);
        }

        private static FluentConfiguration Configurate()
        {
            var fbc = new FirebirdConfiguration();
            return Fluently.Configure()
            .Database(fbc.ShowSql().ConnectionString(GetConnectionString()))
                .Mappings(m => m.FluentMappings
                    .AddFromAssemblyOf()
                )
              .ExposeConfiguration(BuildSchema);
        }

        static void Main(string[] args)
        {
            FluentConfiguration fluentConfiguration = Configurate();

            Configuration cfg = fluentConfiguration.BuildConfiguration();
        }
    }
}