Hi rslay!
Understanding the posting entries of a bank deposit and knowing how your invoice and payments post to your accounts is a way to gain more confidence in using QuickBooks. I'm happy to shed light on this in addition to my colleague's answer.
About your question, the money was already posted to your income account when you created the invoice, so the payment shouldn't post to it again. Instead, it offsets the balance of the A/R, and therefore you see the A/R account on the deposit in your bank register.
For comparison, it's different when you handle downloaded deposits on Bank Feeds. You can directly categorize them as income. Thus, the income account will appear in the bank register. The same principle also applies to sales receipts that are directly deposited into a bank register.
On the other hand, you may want to check about transaction journals to learn more about checking the posting accounts of your transactions.
We're just around if you have more questions about this, or if you need some clarifications on the transactions in your books.
