How to record a refund of a payment

It is a bug in Manager discussed Goods return (Cash sale/purchase) causes Gross Sales error - #22 by Patch and Why do the costs on a journal entry show in the net sales column? - #60 by Patch

The only way to work around it in Manager is to open the suppler tab and open the Debit note tab and enter the return way.

An easier way is to give up on Managers abilities to correctly maintain accounting records, create the custom report it the first link above and manually correct the accounting records prior to submission.