Just edit the original invoice.  Or create a new invoice for the difference.

I can't edit the invoice as the original invoice was in January and we are now in May.  We can't change a prior period.  I guess it makes sense to just create a new invoice in the current month so that there's an invoice in the system to offset.  It's too bad I have to create an invoice in order to post the additional amount in the check.  Was hoping there was a way to add a line to the deposit for the freight as it wasn't technically invoiced but there doesn't appear to be a way to do this.  Thank  you for your quick response.

Creating a new invoice will definitely work, and gives you a good audit trail. But you can post additional amounts when receiving payment against an invoice. After marking the invoice paid, just click over to the Apply To Revenues tab. You can enter additional amounts and post them to whatever GL account you want. The Receipt Amount in the upper part of the screen should reflect the total amount received.