How to post payment to open invoices from a bank deposit

Thanks for your help!  I am a complete newbie to Quickbooks. I did all the steps to the T by going to the deposit and adding the customers/ selecting A/R  and then going to the Receive payments and applying the credit to the open invoice but  I did notice that on my checkbook  register after I finished marking the payments thru the receive payment instructions- apply credit,  that my register for checking shows the payment as A/R again on the register.  This looks to me like like I received the money twice, once in the deposit as A/R and then again thru the receive payment.  This is making my Quickbooks balance go up way higher than my actual checking account balance.  Before I started marking the payments received, both balances matched.  Any insight would be most helpful.