Hi @usertomasz-szlachta
It's a couple of years since I set up the last account but you should be able to enter old transactions & close the old VAT periods so that the new (MTD) VAT periods are correct.
From memory, once you set up your VAT start date (VAT > Edit VAT > Effective date for new scheme) you will have a list of old VAT quarters - you can then check them individually & Mark as Filed without sending to HMRC.
It's possible that you will need to disconnect from MTD temporarily in order for the Mark as Filed option to appear.
Hope this helps.