Hi @Davidwilman
Personally, unless the deposit & refund are on different bank (or card) statements I wouldn't bother recording both - just record as a single nett payment of £138.06.
If you really want to show everything, you can enter the £500 as a Bill Payment (or a Cheque or Card Expense into Accounts Payable with NoVAT code). This creates a credit of £500 against the Supplier.
Enter the Bill as usual for the rental.
Enter a Deposit (or Credit Card Credit) against Accounts Payable again using NoVAT. This creates a Debit of £361.94 against the Supplier.
When you now go into Pay Bills you will see all three amounts - select all to close each one.
Hope this helps.