Overview
For invoices that are not going to be paid, you will need to create a credit memo that will be used to cover the open balance of the selected invoice(s). To do this:
Open the Sales Returns & Customer Credits list in the Sales module and then select Create > New.

When creating the new document, make sure that the type is set to "Credit Memo". You can use a GL Expense via the Expense tab for the amount that needs to be written off. At this point, you can either link an invoice or leave the credit memo unattached.

Where the credit memo says "Apply automatically", choose "Apply manually" and an "Allocate credit" window will open.

Select the invoice(s) that need to be written off, and then select "Apply".
Save and close the credit memo.