You can do this by going to the + icon > expense and select the sales account in the category menu (the income accounts are at the bottom of this menu). This will still allow you to use the purchase VAT codes as normal.
Even if you select a customer in the payee field, you should still be able to select purchase VAT codes. The category will be whatever sales category you would like to use. After saving the transaction, does it post to Box 1 or Box 4 in your return?
I've read your original post. In this case, you'll need to create a journal entry and select the VAT code for purchases, so it will reduce the customer's balance.
Let me show you how:
You'll have to ensure the VAT amount on the journal entry is the same as the invoice. I'll also recommend reaching out to your accountant for further assistance.
I've attached some screenshots below, so you'll know what I'm referring to.
I'm linking an article that will provide you with some tips in creating a journal entry.
Please let me know how it goes by leaving a comment below. I'll be here to keep helping. Have a good day.