Credit Notes in Invoxy are for applying one-off lump sum credits to your clients. This would generally only apply to permanent fees being credited, as any timesheet issues should be corrected in order to keep proper track of margin in your account - see Time Credits for information on crediting time.
Once the draft invoice is created, modify the text in the invoice header to note that it's a credit rather than an invoice.
Alternatively, if you find you need to issue credit notes often you may prefer to create a separate invoice template. That might look something like this:
Adding a Subtotal Group filtered to 'Credit Note' (as pictured) will ensure that using this template for an Invoice Batch will only pull in Credit Note type placements.