Understanding How it Works with WooCommerce
The key to understand is that everything about your customer’s e-commerce experience on your site is still handled by WooCommerce. NS FBA doesn’t duplicate or replace any functionality from payment gateways to coupons to checkout to even shipping methods (see more on mapping Amazon shipping speeds to WooCommerce shipping methods here: http://neversettle.it/documentation/ns-fba-woocommerce/how-to-use-shipping-speeds-woocommerce-fba/ ). Because of this, NS FBA is compatible with any WooCommerce extension including payment methods.
The way NS FBA works is that it silently monitors WooCommerce in the background and detects when an order has been completed and paid for. Then, it takes that order information and looks for products that you have set to fulfill with Amazon. It will send the data for those products by SKU along with the order information like shipping address to Amazon Fulfillment where FBA then takes over and ships the items. NS FBA will detect any errors with the FBA shipping request like if a SKU is out of stock in Amazon, create an Order Note about the issue, and send you an email about the problem.