This is why I pay my fees and most everything else with PayPal.
For now I suggest using PayPal balance from sales to pay fees.
Do you pay your seller fees only once a month? I prefer to pay them daily with PayPal and clear them off before the fees get to high. My fees can be $1500+ there is no way I would pay that with one hit on a credit card
For the new payment system I think they have all in one fees system I'm not sure though if they auto deduct the fees from each batch of daily sales processed. But I think you will still be able to pay fees with PayPal.
I HATE credit cards and banks