When creating an AR Credit Memo it will only let you apply it to one invoice. These are instructions on how to apply it to multiple invoices.
After you create the Credit Memo and apply it to the first invoice, click payment in the AR Console.
Select Cash as the payment Method. In the Invoice/Payments selection, select the Credit Memo first and add it to the transaction.
Then start adding invoices to the transaction that you want to apply the credit memo to. You can select as many as you need to use up the amount of the Credit Memo. If the last invoice you select to apply the Credit Memo to is not the exact amount of the remaining balance of the Credit Memo, then you need to manually change the amount to apply before adding it to the transaction window. Notice that when you select the invoice it shows the full amount due of the invoice, which doesn't match the amount left to apply from the Credit Memo.
Change the amount to add from the invoice to the transaction to match the remaining amount of the Credit Memo and then click QuickAdd.
Now the Applied Total and the Unapplied Total both equal zero. Click OK on the transaction and you are done.