It is up to the seller. Look at the listing, does it say that the seller will only accept payment by Paypal? Or does it say you can pay by paypal, cheque, card etc? If it does, select pay by card.
I once bought an item and I didn't have enough money in my paypal account, paypal took the balance left in my account to make part payment, and the rest came off my card. I just waited until the transaction was complete and then transferred some money back into my paypal account.