1. Within QuickBooks, click Receive Payment at the top.
  2. Select Accounts Receivable Import at top left.
  3. At Deposit to drop-down, select Unapplied Cash.
  4. Go to the first Outstanding Transaction.
  5. Select the Credits.  The amount received will likely be a negative amount, assuming there are more credits than the single selected debit.
  6. Select additional Outstanding Transactions until the amount received is positive.
  7. Save and close the transaction.  There is now an Unapplied Cash posting that must be cleared.
  8. Add a Journal Entry to debit A/R and credit Unapplied Cash for the payment amount above.

The instructions above are only for clearing open invoices, a very specific task.  
For information more detailed information about invoices, click here and see pages 18 - 20 of the EZLynx Accounting User Manual.