table Company
{
int SysId
...
}

Premise
{
int SysId
...
}
CompanyPremise
{
int CompanyId,
int PremiseId
/*Both form composite primary key*/
}

Entity calses
public class Premise
{
public Premise( )
public virtual  IList<CompanyPremise> CompanYPremises{ get; set; }
....
}
public PremiseMap()
{
      Table("Premise");
      LazyLoad();
      Id(x => x.SysId).GeneratedBy.Identity().Column("SysId");
     .....
    HasMany(x => x.CompanyPremises);
}

public class Company
  {
    public Company()
    {
    }
    public virtual int SysId { get; set; }
    public virtual IList<CompanyPremise> CompanyPremises { get; set; }
...
}

public class CompanyPremise
  {
    public CompanyPremise() { }
    public virtual int CompanyId { get; set; }
    public virtual int PremiseId { get; set; }
    public virtual Company Company { get; set; }
    public virtual Premise Premise { get; set; }
}

public class CompanyPremiseMap : ClassMap<CompanyPremise>
  {

    public CompanyPremiseMap()
    {
      Table("CompanyPremise");
      LazyLoad();
      CompositeId().KeyProperty(x => x.CompanyId).KeyProperty(x => x.PremiseId);
      References(x => x.Company).Column("CompanyId");
      References(x => x.Premise).Column("PremiseId");
    }

  }

public CompanyMap()
    {
      Table("Company");
      LazyLoad();
      Id(x => x.SysId).GeneratedBy.Identity().Column("SysId");
      HasMany(x => x.CompanyPremises);
}

var trans =session.BeginTransaction();     
var cm = session.Get<Company>( companyId );
      var pm = session.Get<Premise>( premiseId );     
      var cp = new CompanyPremise
      {
        Company = cm,
        Premise = pm       
      };     
      session.SaveOrUpdate( cp );
transaction.Commit();