According to the manual page 19 (you have read it right?) ... slots PCI-E 2 and PCI-E-3 can be used with two graphics cards in SLI or crossfire. They will both get x16 system access width.
You could put a x1 card (network, sound, other low bandwidth card) in a x16 slot. It will work. The x4 slot would typically be used for a RAID controller or a 10GE card.