I am unable to apply a credit memo which is sync by Webgility? How to apply a credit memo manually?

Hi @Rizwan Sharif , 

Thanks for visiting the QuickBooks Community. Allow me to help you apply a credit memo to your customer’s invoice in QuickBooks Online.

If a customer paid more than what was owed, returning a product, requesting a refund, or if you’re rewarding them with a store credit, you can create a Credit Memo. Once done, you can apply it to an open invoice for a given customer. 

Here’s how to create a credit memo in QBO:

1. Click the Plus (+) icon and select Credit Memo.
2. Choose the customer name.
3. Enter the Credit Memo Date.
4. Fill in the necessary information.
5. Click Save and close.

However, if you have already created a credit memo, you can proceed in applying it to the invoice. Follow the steps below on how:

1. Click Sales from the left pane.
2. Select Customers and click the customer’s name.
3. Locate the invoice you want to apply the credit to and click Receive Payment.
4. Enter the necessary information on the Receive Payment window.
5. In the Outstanding Transactionssection, make sure that the correct invoice is selected.
6. Click Save and close.

The steps above will help you apply the credit to your customer’s open invoices. For your reference, you may check out this article: Apply credit memos . Comment back, cheers.