You can't transfer between Stripe accounts. Charges going through Connect have the same fees as ones not going through connect (namely, 2.9% and $0.30).

If you're using our application_fee parameter to take your own fee out of a transaction, you get the full amount you request. Both that full amount, and the Stripe fee for the charge, are subtracted from the total amount paid to the seller.

To illustrate, a $100 charge with a $1 application fee would end up sending $1 to the application, $3.20 to Stripe, and $95.80 to the seller.