I've been using Quickbooks Self Employed with my Etsy store for a while now, and this issue is still an annoyance.
When my orders are processed via Quickbooks from Etsy, the order total (including postage cost) is added, then the Etsy processing fee's are deducted. However, it seems that the cost of purchasing postage labels (I'm using Royal Mail, not Etsy labels) is not being deducted, and I'm having to add it manually as a lump sum at the end of every month now.
Is there an option to solve this? I would rather it be done automatically, than me having to manually enter it at the end of the month. All other fees are being processed by Quickbooks fine, it seems, except postage.
You can contact the Technical Support of Etsy so someone can help you map the accounts of your transactions, correctly. This way, it'll automatically be downloaded into your QuickBooks account so you won't need to enter them manually.