Welcome to the QuickBooks Community, jj.

Yes, you can apply payments from one check to several customers in QuickBooks Online. Let me walk you through the process to achieve this efficiently.

I recommend creating a bank deposit in the application, which allows you to enter different entries or payments and assign them to various customers and accounts.

Here's how:

1. Click the + New button and choose Bank Deposit.
2. Go to the Add funds to this deposit section.
3. In the Received from column, select different customers.
4. From the Account dropdown list, choose the separate account you want to put the money into. Note: You can select Accounts Receivable so you can use the amount to apply to an existing invoice.
5. Select Check as payment method.
6. Enter separate amounts to indicate payments for a different customer.
7. Fill in other needed fields.
8. Click Save and close.

In case you need steps on how you can record partial payment for an invoice, you can read this article: Record invoice payments in QuickBooks Online.

If you have other concerns about managing customer payments in QuickBooks, don't hesitate to visit the Community space anytime. As always, I'll be around to help you out again, jj.