According to GAAP accounting principles, invoices are not added to the Invoices Export Queue until they are marked Shipped in Allmoxy.
Payments made in Allmoxy are also automatically added to the Export Transactions Queue for export to your financial software. You can export this file and import via Saasant or Transaction Pro into your financial software. 
If you require payment before processing an order, you will have received payments that will be available to export into your financial software before an invoice is created in your financial software.
If you accept payments in your financial software, then manually record them in Allmoxy, do not use the Export Transactions Queue. This will cause duplicate payment entries in your financial software. If you want to accept card payments through Allmoxy, then record manual payments in Allmoxy first and use the Export Transaction Queue to update your financial software of all payments.
Reconciling Invoices and Payments
If you choose to not accept payments exclusively in Allmoxy, you'll need to reconcile your Allmoxy payments to your accounting software. The best way to do this is to use the Export Transactions Queue and cross-reference your financial software to ensure all payments in Allmoxy and recorded properly.
If you're processing payments via Stripe, you'll find that the amount deposited into your bank account differs from the customer's payment amount. This is due to Stripe's per-transaction fee that is deducted before the money is paid out to you. To reconcile this amount, log into your Stripe Dashboard, navigate to reports, find the payout report that reflects the Stripe fees deducted. Enter the Stripe fee as an expense or as a journal entry in your financial software.