On Receive Payment screen (create + sign > customers > receive payment) > select deposit to: undeposited funds > choose invoice and payment amount > save
Next step > On Bank Deposit screen (create + sign > other > bank deposit) > select customer payments > match total payment to bank deposit > save
If you are downloading bank transactions > banking center (left navigation bar > transactions > banking) > click deposit in question > deposit transaction screen will expand > select “Find Match” > select transactions (payments) to match deposit amount > save
Click on the screenshots below to enlarge them
#QuickBooks Online