Hi Benny,
If you add it to (1) (i.e. “WooCommerce > Settings > Cost of Goods > Extra Costs: Payment Gateways”), you will get an approximate fee value, e.g. 5% for each order.
If you add it to (2) (i.e. “WooCommerce > Settings > Cost of Goods > Orders > Extra Costs: From Meta”), you will get the exact value that is automatically sent to WooCommerce by e.g. PayPal. For PayPal, you should set the option to (I know it doesn’t look like a proper meta key, but it is how PayPal fees are saved in WooCommerce):
PayPal Transaction Fee
To sum up – you should use either (1) or (2), otherwise, you will get a 5% + PayPal fee, which is not what you need probably.
Hope that helps. Please let me know if you have any questions.