It looks like you are using the Accounts Receivable register to enter receivables. You should be entering Invoices or Sales Receipt.s If they are paying right away or have paid, you use Sales Receipts. If they are paying later, use Invoices, then go to "Receive Payments' to enter the payments when they do pay. You would either choose deposit to Undeposited Funds (a preference you set in Preferences) or directly to the bank account ONLY IF it is the total deposit.
The reason the balance is still $961.89 is that the balance on your Accounts Payable was $961.89 before you made those entries. Go Reports, Customers & Receivables, Open Invoices. You can then see who is still owing money, the total of the unpaid invoices should be $961.89.
