How can i make a payment for an invoice , but the payment is already done thorw Manual entry?

We are grateful for your participation here in the Community forum, Ahmed. We would be glad to provide you with the specific details to handle your invoice payments in QuickBooks Online (QBO) properly.

To clarify, have you manually entered the payment using a bank deposit in your QBO account? If you did, we can link that bank deposit to your invoice to keep your records accurate and help avoid errors when it's time to reconcile your accounts.

We can start by locating and editing the deposit transaction in your bank register. Here's how:

1. Go to Settings ⚙, and choose Chart of accounts.
2. Find the account you deposited the payment to and select Account history.
3. Find and pick the correct deposit. Then select Edit.
4. Find the deposit in the Add funds to this deposit section.
5. From the Received From ▼ drop-down, select the customer the deposit was from.
6. Choose Accounts Receivable in the Account ▼ drop-down.
7. Tap Save and Close.

After that, follow these steps to apply it as a credit to the invoice:

1. Click the + New button and select Receive payment.
2. From the Customer ▼ drop-down, select the customer’s name. This displays all unpaid and outstanding credits for your customer.
3. In the Outstanding Transactions section, choose the invoice you must mark as paid.
4. In the Credits section, pick the deposit.
5. Complete the necessary fields and, tap Save and close.

However, if this isn't the case, can you please share additional information on what you're trying to achieve within the QBO program?

Additionally, you can check out this article as your reference for receiving and categorizing invoice payments in QuickBooks Online: Record invoice payments in QuickBooks Online.

The Community is always open if you have other questions while working with your QBO account. I'll be around to help. Have a great day ahead!