In this scenario, a customer has a monthly pest service and a yearly pest service. The customer sends in a payment for the yearly service prior to it being done, and prior to creating an invoice. You want to post the payment but not automatically apply it to the monthly pest service balance.
Create a new Payment
Enter an amount and Save & Apply
When the Invoice is generated, apply the Unapplied Payment to it
Open the customer's account
Click Create a New...
Choose the payment method
Enter the amount
For Reference # you might want to mention Yearly pest service advance payment, or something like that
Enter the Receipt #
Click Save & Apply
You will see under Unapplied Payments the amount the customer paid. This serves as a credit to the customer's account.
Once the yearly pest service Invoice is created apply the Unapplied Payment to it.