You use the Receive Payment option anytime you need to apply a payment to an existing invoice. Receive Payment posts a payment to your customer's Accounts Receivable (A/R) account. Creating an invoice increases A/R and receiving a payment decreases A/R. So, if you issue an invoice that increases A/R, you need to use Receive Payment on that invoice to reduce it and show it as paid-in-full or partially paid if that's the case.
You can also use Receive Payment before issuing an invoice. QB will create a credit that can be applied to a future invoice.