The processing fee that Stripe charges is fixed and is deducted from the money paid by your client (invoice payment total). Stripe charges a percentage of the total transaction value plus a minimal fixed fee per transaction for using ePayments. The percentage and fixed fee varies by country and currency. You can check out the Stripe processing fees here for your country.
The processing fee that you specify in Global Settings gives you the ability to pass on some or all of the Stripe fee to your clients.