Hi Mike,
1. Extra field to manually add the shipping expenses – I believe what you need are “Extra Costs: Per Order” options in “WooCommerce > Settings > Cost of Goods > Orders”.
2. Display it in the report – already working on it. Will be added in the next plugin version. It’s planned to be released this week.
As for automatically subtracting the PayPal fee from order profit – this is not done yet, however, I will try to add it to the plugin as well. Meanwhile, you can use the “Payment fee” option in the same “Extra Costs: Per Order” section, however, you will have to manually enter the fee for now.
Hope that helps. Please let me know if you have any questions.