QuickBooks Point of Sale & QuickBooks Enterprise

First, you should create an item for bounced checks, canceled credit card payments, etc.
 
    1.    Go to the Lists menu and click Item List.
    2.    Click Items at the bottom of the list and then click New.
    3.    Create an Other Charge item titled something like "Returned payment"
            -In the Amount field, leave a zero amount.
            -From the Tax Code list, choose Non.
            -In the Account field, choose your bank account (for example, Checking).
    4.    Click Next.

If you want to charge them a service charge for bank fees, etc. create another item:

    5.    Create a second Other Charge item titled something like "Service charges"
            -In the Amount field, leave a zero amount
            -From the Tax Code list, choose Non.
            -You have two options for Account. If you are merely passing on your bank charges, you may want to use your bank fee expense account (this will reduce your bank fee expenses). If you are charging more than what your bank charged you, you should probably create a revenue account called something like Service Charges instead.
    6.    Click OK.

Then use these items to re-invoice the customer:

    7.    Go to Customers > Create Invoice
    8.    For the first line item on the invoice, use the returned payment item for the amount of the amount of the reversed payment. Because this item is linked to your bank account, this will reduce your bank account by the amount of the bounced check, thereby backing out the original transaction on your books. The income for the original sale will be recorded when you receive the new customer payment.
    9.    For the second line item on the invoice, use the Bad Check Charge item for the amount of any bank fees that you want to recover.