Welcome to the QuickBooks family, Karate Dan.
Thanks for being detailed information about your concern. This gives me a clearer view of how to track your transactions.
Based on the scenario, we’ll have to match the imported invoices to the payments. Creating a manual deposit will cause duplication to the entries. Here’s an article that covers the complete steps from downloading the data up to reviewing and matching the information: Categorise and match online bank transactions in QuickBooks Online.
However, if you prefer to enter the deposits, link them to the invoices. If there are downloaded payments, make sure to exclude them. This process will keep your records in tiptop shape.
Here’s how to make a deposit:
- Tap the New menu in the upper left to select Bank Deposits under Other.
- On the Bank Deposit page, click the Account drop-down to choose the bank you want to track the funds.
- Then, type in the correct date of the entry.
- Scroll down to the Add funds to this deposit section and enter the complete details of the entry.
- Click Save and Close.

For additional information about the Bank Deposit feature, see the Record and make Bank Deposits in QuickBooks Online link. It covers the complete instructions on how to manage your funds as well as placing them into the Undeposited Funds account.
To associate the payment to an invoice:
- Choose the New menu in the upper left and pick Receive Payment under Customers.
- This will open the Receive Payment page.
- In the Outstanding Transactions section, mark the box for the invoice you want to link to the deposit.
- Press Save and Close.

Let me share How to link a deposit to an invoice guide for more information. It contains tips when to connect the payment to the sales entry.
To exclude downloaded bank data:
- Go to the Banking menu on the left panel to choose the Banking option.
- Form the list of accounts, pick the account you’re working on.
- In the For Review section, tick the boxes for the payments you want to remove.
- Hit the Batch actions drop-down and click the Exclude Selected option.

To clarify, are you going to process the tax return in QBO or outside the system? If so, I recommend keeping track of what’s happening to the actual transactions in the company. The data generated on the VAT return is based on the entries recorded in QuickBooks. However, if you’re going to file the tax form manually, input the data you want to add in the company file.
I’m adding some articles to help get acclimated about the product’s features, processes, and instructions on how to process a VAT return.
The information I shared will point you in the right direction tracking your income and filing the VAT return.
Keep in touch if you need assistance while working in QBO. I’ll be right here to lend a helping hand. Enjoy the rest of the day.