Pandadoc QB Payments, how do I create an invoice without a double entry

I appreciate you for sharing your concern here in the Community, chris-errcsdesig.

I'm here to help you remove duplicates and link invoices to QB payments in QuickBooks Online (QBO).

First, we'll delete the manually created deposit and then undo the one from your banking.

Here’s how to delete:
 

1. Go to the Accounting menu and choose Chart of Accounts.
2. Locate and click the View register of your bank.
3. Click the manually created Deposit and select Delete.
4. Hit OK to confirm.
    

Undo the added Deposit from the Banking page:
 

1. From the Banking menu, tap the bank where the deposit came from.
2. Choose the Reviewed tab, and look for the deposit.
3. Click Undo under the ACTION column.

After deleting or resetting the deposits, we’ll match the invoice that was already paid to the cleared deposit from the Banking page.
 

1. Still from the Banking page, tick the bank and look for the deposit in For Review.
2. Click the deposit and select Find match.
3. Filter the Date range that includes the date when the invoice payment was created.
4. Check the Payment and then click Save.
    

Once done, try to run the Profit &Loss report again to check if the total is correct.

For future help, here are some links that cover all the details on how to perform the following tasks in QBO.
 

• Record a customer refund in QuickBooks Online
• Handle a customer credit or overpayment in QuickBooks Online
   

Come can visit us again if you have other questions about managing invoices. I'd be more than happy to help. Have a great day!

When I click the "banking" page I get three options: 

Quickbooks Checking - which I do not have 

Capital

PPP center.

There is no other option

Thanks for a quick response, chris-errcsdesig.

Based on your statement above, I figured out that your company file’s interface is set to Business view. Because of this, the steps that my colleague provided above can’t be applied.

Worry less, I can guide you with changing this to Accountant view to proceed with the steps above and enable you to link the deposit to the invoice in QuickBooks Online (QBO).

Here’s how:

1. In your company file, go to the Gear icon.
2. At the bottom right corner, click the Switch to Accountant view to change the interface.

You’ll want to check out this article for a better understanding of the differences between the two: Switch between Business and Accountant view in QuickBooks Online

That’s it! You can then proceed to the steps outlined by DebSheenD and link the deposit.

Moreover, learn from this article to check when QuickBooks deposits customer payments into your bank account: Find out when QuickBooks Payments deposits customer payments

If you have more concerns about deposits, please don’t hesitate to add a reply. Have a good one!

Still does not work, when I click this ( I am in accountant mode ) all I get is a screen to sync my bank account. 

Deleting the deposit and invoice I created was simple, but now I need to create an invoice which shows the deposit made and deposit the payment from qb payments screen. If I do both, I get double deposits. 

Thanks for following up with us, @chris-errcsdesig. 

Since the steps my colleagues have provided aren't working for you, I recommend contacting our Customer Support Team. This way, one of our agents can review your account in a secure environment and investigate this matter further. You can use the link I've included below to connect with our team. 

• QuickBooks Payments Support

Don't hesitate to let me know if you have any further questions or concerns. Have a good one!