Since Magento is an online store with a different type of payment processing account type than your brick and mortar store, all credit card payments are captured and processed in Magento. The payment details are downloaded into the point of sale in the Shipping/Printed Notes section of each sale.
Payments in Lightspeed Onsite
Most point of sale will apply payments automatically, however, payments in Lightspeed Onsite cannot be applied automatically and must be applied manually. We suggest using the Magento payment method to make reporting of online sales within Lightspeed Onsite as simple as possible.
Since payment is captured in Magento, the Magento Payment Method should be applied to all downloaded Magento Orders and Credit Memos in Lightspeed Onsite.