My problem comes when I send an invoice to a customer and they pay with a credit card through stripe. It all gets credited and such and I like that. But then when I update my bank feed after I have transferred my balance from Stripe to my bank account, now I have this duplicate charge. 

Am I supposed to just exclude this everytime, since the payment was already recorded in the system when they paid? 

Also, should I make any corrections for the fees that stripe charges? Overtime will I see a discrepancy with the books if I never make an entry for "fees paid to stripe"?