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The schematic is just a diagram of the circuit. The PCB is the physical representation of the circuit. You need to pick a physical LED that you will solder to your finished PCB and select the footprint (from any of the ones shown or make your own) that will fit the component. Any one of these shown can be considered a "generic" LED footprint. If you're just playing around with the system and don't plan on actually making a PCB, you can use any of them.