I didn't see anyone address your question. The answer is yes. You have to calculate the fee twice, then add that fee to the new line to end up at the exact amount you intended to invoice. It's a PITA.

As an example, $100 invoiced and paid with ACH is $100 x %1.0 = $101.00... but if you add a line for a $1.00 fee, the total fee is calculated on the $101.00 and you will end up with $99.99 after the fee. You have to invoice $101.01. It's the most ridiculous thing. Here's a google spreadsheet with what we setup.

https://docs.google.com/spreadsheets/d/1SnaR3GDiw8CFMpTn6XRn12o1xX5OrCuHdiCuwvoNNcA/edit?usp=sharing