I have this same exact issue except mine goes a step further. I use wix along with the quickbooks app to automatically track my invoices generated from sales. The issue is that these payments are made to wix and wix charges a 2.9% POS processing fee plus $0.30 to the total before depositing this into my account. For instance a sale of $52.98 on the invoice is deposited by wix as $51.14 after they take their $1.84 out. So I have to go in and link each one manually, calculate the difference, and post as a separate transaction? There has to be a better answer, this should be a pretty  common issue with wix and quickbooks but I cant seem to find the right article.