You can apply for Flat rate scheme at the time you register for VAT, or any later time; not EARLIER. If you apply near the time of your VAT registration, you can start using the scheme from the date you are registered for VAT.
HMRC will notify you in writing if your application is successful. The letter will tell you the date you can start to use the scheme. This will normally be from the start of the VAT period following receipt of your application. If you request an earlier or later start date, HMRC will consider all the facts including the timing of your application and your compliance record. They will NOT normally allow you to go back and use the scheme for periods for which you have already calculated your VAT liability.