Once you submit an MTD VAT return or confirm a Legacy VAT return, the system will generate a sales invoice from your HMRC contact if you are owed money, or a bill to your HMRC contact if you owe money to HMRC for VAT. 

The double entry of the bill for VAT owed to HMRC will Dr VAT control and Cr Trade Creditors. 

The double entry of the invoice for VAT owed from HMRC will Cr Vat control and Dr Trade Debtors.

If you would prefer the system to create a journal instead of an invoice, keeping the balance out of creditors and debtors, you can toggle on the VAT return journal feature on the Settings > Configure system > Toggle features > Accounting menu:

The journal created by the system will either Dr/Cr VAT control and Dr/Cr VAT payable depending on if you owe or are owed money for VAT. 

When you account for your payment to HMRC make sure to use the VAT payable account.