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. 

If you would prefer the system to create a journal instead of an invoice, you can toggle on the VAT return journal feature on the Settings > Configure system > Toggle features > Accounting 

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.