CIS to run independently of PAYE

Why can CIS not run at a deiferent time to PAYE and still maintian the details under the same company and also automatically deal with the filing with HMRC and updating HMRC of PAYE/CIS due without any manual intervention. MoneySoft Payroll Manager a produce far inferior to paycircle can so I am amazed that paycircle doesn't handle this better/more 'slick'.