Firstly, matching the Amazon sales up between the two types of reports from Amazon (Settlements and Business Reports) is never an exact match.
Link My Books uses Amazon's settlement reports which breakdown each of the payouts you have received from Amazon into their transaction line items like:
The business reports in seller central only show the principal part, ie. they don't include shipping, gift wrap etc. just the item price element of orders.
The business reports also show the figure inclusive of any VAT where as your P&L sheet in Xero or QuickBooks will show sales excluding any VAT.
So if you are trying to compare your Amazon business reports sales total with your sales totals showing in your accounting software after pushing your settlements over from Link My Books then this is pretty much impossible.
Lastly you also have the time difference to account for as the business reports and settlement reports don't account for orders in the same way. The business reports use the time stamp of the order where as the settlement report only includes the order once it has been paid, which often doesn’t happen until it is dispatched.
How can I trust the data coming out of Link My Books then?
Rest assured that since we are using Amazon's own settlement reports and those are a full breakdown of all the transactions that make up each payout you receive from Amazon - you can trust that the data is 100% accurate.
The invoices we post to Xero and the sales journals we post to QuickBooks are simply a summarised aggregated version of the settlement reports from Amazon which will always match exactly the payout you received from Amazon.