It's vital that all your transactions be entered correctly so that your books can be well balanced. QuickBooks Online is a great tool able to help you keep track of your invoices and payments so you can see your customer balances. I can point you in the right direction to enter this payment.
In order to apply this cheque you received to multiple invoices, you can create it as a payment by going to the Sales tab, then Customers. Find the customer in question, then click on their name to see their transactions. Select Receive payment option next to the invoice you want to pay, then in the list of available payments, check the ones you want to apply the cheque towards.
If you have any other questions, feel free to reach out here.
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