Any payments taken through your Magento site will automatically download along with the order. This means the sales order will be marked as paid and the necessary accounting will be created (sales receipt). At the moment we don’t get enough information from Magento to identify which payment method was used, so all order payments will be added to the same bank account. In the future we plan to support different accounting streams for each payment method, so you can track PayPal revenue differently from Sagepay, for example.
Tips:
When you're setting up payment methods in Magento, such as Authorize.net, you will need to select the Payment Action to specify whether you want to "Authorize Only" or "Authorize and Capture" the payment. If you wish to actually take the payment off the customer at the point they process their order you should select authorize and capture, authorizing only will allow you to take payment at a later date.
