Hi there estevangcoc,
Making sure that your deposits are entered correctly is an important step so that your bank balance is correct. QuickBooks Online is a great tool to help you keep an eye on money movement in your bank account. I can provide some assistance with this.
The best way to record payments that end up being deposited as a batch would be to send the payments to Undeposited funds, then creating a Bank deposit to move them from the Undeposited funds to your bank account. When creating your Payment, select Undeposited Funds as the Deposit to account. Then to deposit the transactions, click the Gear Icon, then Deposit. Check the transactions that make up the deposit, then Save.
Here's an article that goes over the process of making deposits in QuickBooks Online.
If you have any other questions, feel free to reach out here.
