What is a FDD header in computer terms?

FDD (Floppy Disk Drive) headers are used for floppy disk drives. In all likelyhood, you won't be using them. IDE headers are used for CD/DVD drives and older hard drives, and SATA ports are used for newer hard drives. As far as USB ports *on* the motherboard? You mean the ones on the back? Those are just for peripherals.