Hello @dhavalkakadiya,

Thank you for posting here in the Community. I can share some steps to help you correct the unapplied payments in QuickBooks Desktop.

You'll need to link the deposits to your open invoices in the system. This keeps your records accurate and helps avoid errors when it's time to reconcile your accounts.

First, you'll need to find and make changes to the deposit. You can find the transaction by opening your bank register in the chart of accounts.

Here's how:

1. Click Lists.
2. Go to Chart of Accounts.
3. Double-click the bank account, then look for the deposit.
4. Open the transaction.
5. Change the account to Accounts Receivable.
6. Hit Save & Close. 

Once done, you can proceed with applying the deposit to the invoice. Please open the transaction and press the Receive Payments option.

Follow these steps:

1. Open the invoice.
2. Select Receive Payments. 
3. Click Apply Credits at the bottom.
4. Choose the deposit.
5. Hit Done.
6. Press Save & Close.

You can pull up the Profit & Loss Detail report so you can see the categorization. You can use these steps:

1. Click Reports.
2. Go to Company & Financial.
3. Select Profit & Loss Detail.

Also, I've attached an article you can use to learn how to correct and re-apply payments that were applied to the wrong invoice in QuickBooks: Resolve common issues when applying a payment towards an invoice.

Keep us posted if you need anything else regarding the process. Have a great day.