The invoice and the cover letter can be sent together using the individual mail merge or Print/Email Mail Merge feature under the Actions menu on the main Invoice Grid. Be sure to filter the grid to include only Unpaid or Partially Paid invoices under the Status column.
You can choose to create just the Mail Merge Template and do not select an attachment. Or, choose the attachment and select Skip Page 1 under Format. This will produce just the invoice, not the cover letter. A Mail Merge Template must always be chosen, regardless of whether it is printed or not. Complete the rest of the fields and click "OK" to complete.