Amazon FBA & Amazon MFN and balancing at the end of day

Good day everyone. 

Important details


We ship in to Amazon FBA with dry goods outside of shopify's ecosystem

We also sell as "seller fulfilled" using the amazon sales channel on Shopify


I'm struggling trying to seperate the fees for book keeping. 


So when an item sells on Amazon as seller fulfilled using our amazon sales channel Shopify shows the sale on the financial summary that we use at end of day, but the # it reports is the sale total, including Amazon Fees that are taken away. And we should not be paying tax on those. 

I've considered just scratching out the 'total payments' and editing the number to be less the amazon MFN sales so I can balance without Amazon. Has anyone faced this issue and how did you deal with it?

1 year e-commerce, 7 years B&M store.