Yes, Pipemonk does support payment fee tracking in a scenario wherein a store is using multiple payment gateways.
Do you want to track Payment Fees? Yes/No
Enable this option if you want to use both Shopify Payment Gateway and PayPal Gateway for payment.
To handle payment fee for a particular payment gateway, Pipemonk depends on JSON from Shopify. If Shopify provides JSON for a payment gateway, we track payment fee for it.
For more understanding, contact Customer Care at support@pipemonk.com!!