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I'll provide the proper or the usual flow for receiving a check payment for an invoice without bloating your Balance Sheet.
The first thing that you want to do is to open the invoice and click Receive payment.
QuickBooks routes you to the Receive payment page, where you enter the payment details. Watch out for the Deposit to field. You'll want to choose your checking account to directly post the payment there or use Undeposited Funds so you can deposit the transaction later on.
If you've selected Undeposited Funds in the Deposit to field, deposit the payment using the steps below. Do this after endorsing the actual check to your bank.
Since the transaction is also downloaded on the Banking page, it should autodetect the bank deposit (last transaction in the process) you created. You just have to confirm it.
It's important that all transactions are connected to avoid doubling your deposits. The invoice is linked to the payment, the payment is linked to the bank deposit, and the bank deposit is linked or matched to the downloaded transaction.
Remember that you can always delete and recreate a manually entered payment and bank deposit transaction if you notice that the numbers are not adding up.
I'm just around if you need more assistance with your transactions.