If it's Pilot/Flying J specifically then you do need a Flying J card. On the diesel pumps you swipe your PFJ and then pay inside after you pump. You receive a 3 cent per gallon discount and you can use your CC but pay the cash price.
If you pump from the RV pumps (gas or diesel) you first swipe your CC and you will be asked to swipe your PFJ card. You must do it in this order to receive the discount and if you don't you can't get the discount after you pump. If you have any questions BEFORE you pump just go inside and have them turn it all on for you.