1. All VAT transactions must go through the sales ledger, purchase ledger or VAT Adjustment functions to be recorded on VAT reports or included in VAT return submissions.

2. Fuel scale charges are an addition to Output tax and therefore need to be put through the Sales Ledger. To do this, raise an invoice on a Sundry Sales Account analysed to a sales analysis code linked to a vehicle expenses nominal account and a standard-rate VAT code, and enter the scale charge as the goods total and the VAT due on that as the VAT amount (it is not actually 20.0%). This will result in VAT due of the specified amount, a reduction in the vehicle expenses of the scale charge and an additional debtor of the invoice value. To clear this debtor and adjust the vehicle expenses, enter a journal crediting the Sundry Sales Account and debiting the Vehicle expenses account with the total invoice value. The final result will be VAT due of the specified amount and an increase in vehicle expenses equal to that VAT amount.

From How to fill in and submit your VAT Return (VAT Notice 700/12):

• Box 1 VAT due in the period on sales and other outputs
  fuel used for private motoring where VAT is accounted for using a scale charge
• Box 6 total value of sales and all other outputs excluding any VAT
  fuel scale charges

See Motoring expenses (VAT Notice 700/64)

3. Purchases of Goods and directly-related services from ouside of the UK. Supplier must be flagged as EC Member State or Non EC Member State. Goods must be entered as exempt, zero-rated or standard as if purchased from a local supplier. The item must be flagged as Goods or directly-related services.  When booking a Purchase Invoice or Credit Note onto axis diplomat the user will be required to select whether each line for 'Goods and directly related services' is applicable for Reverse Charge or is an Import. Reverse charge is applicable on imports of goods and directly related services of £135.00 or lower. If Reverse Charge is selected, axis diplomat will calculate the reverse charge VAT. The value of the reverse charge VAT will be recorded in Boxes 1 and 4 on the VAT Return. The value of the inputs will be recorded in Boxes 6 and 7. 

4. Purchases of Services from non UK suppliers into England, Scotland or Wales. Supplier must be flagged as EC Member State or Non EC Member State. Goods must be entered as exempt, zero-rated or standard as if purchased from a local supplier. The item must be flagged as Services. axis diplomat will correctly calculate the reverse charge VAT. The value of the reverse charge VAT will be recorded in Boxes 1 and 4 on the VAT Return. The value of the inputs will be recorded in Boxes 6 and 7.

5. Sales outside the UK fron England, Scotland or Wales. These are zero-rated. The customer should be flagged as either EC or Non-EC Export Customer. The value of outputs will be recorded in Box 6 on the VAT Return.

6. Invoices for VAT from shipping agents for other imports - goods value zero, VAT amount is invoice value. The VAT is normally the standard rate on the import value, and should be booked against a standard rate code but with a goods value of 0.00. The invoice(s) for the imports and any associated charges should also be booked to a standard rate code, but with a zero VAT amount. A special VAT code for standard-rated non-EC imports could be used, allowing identification of such transactions. The value of inputs will be recorded in Box 7 on the VAT Return.

7. Postponed Import VAT is accounted for in boxes 1 and 4 on the VAT return. See our Postponed Import VAT support note on how to use VAT adjustment transactions to account for this on your MTD VAT Return.

8. Bad Debt Relief. For those customers not running Cash VAT Accounting or a Retail VAT scheme, VAT reclaimed needs to go into Box 4 - Reclaimed on Purchases. Therefore journal the amount of the bad debt from customer account (CR) to a Nominal Ledger Bad Debt Account (DR). Then use Purchase Invoice Booking to enter an invoice on Supplier Account Bad Debt Relief for the amount of the VAT to be reclaimed. Analyse goods value of 0.00 to the Bad Debt Account, and a VAT amount of the invoice value at the standard rate. Then journal the VAT amount, debiting the Supplier Account, Bad Debt Relief, and crediting the Nominal Ledger Bad Debt Account. The end result is an increase of the VAT in box 4, 0.00 balances in the Customer and Supplier Accounts, and a debit value in the Bad Debt Account of the original bad debt less VAT. Refer to https://www.gov.uk/guidance/relief-from-vat-on-bad-debts-notice-70018 for further information.

9. Repayment of input tax when supplies are not paid for (clawback).  Input tax due for repayment when you do not pay a supplier needs to go into Box 4 - Reclaimed on Purchases therefore use Purchase Credit Note Booking to enter a credit note on the supplier account for the value of the invoice(s) that have not been paid. Use Manual Payment Allocation to allocate the credit note against the invoice(s) to be written off. Refer to https://www.gov.uk/guidance/relief-from-vat-on-bad-debts-notice-70018 for further information.

11. Other VAT adjustments. Any other adjustments required for your VAT return should be entered using the Adjustments to Output VAT and Adjustments to Input VAT functions. Videos on creating adjustment types and using these functions are available at https://www.axisfirst.co.uk/software/making-tax-digital/axisdiplomat/video/