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A Cisco trunk port can send and receive frames both with and without a VLAN tag. The native VLAN correlates what VLAN the untagged frames belong to.
There's no one main purpose for this feature, but it's useful in some special cases where, for some reason, you have both tagged and untagged frames.
No, you don't have to configure it. When you don't, the Cisco default is VLAN 1.
When you have a VoIP phone and PC on the same data jack, it's pretty common that frames to/from the PC are untagged, but frames to the VoIP phone are tagged. This so we can have both a data VLAN and a VoIP VLAN.
On a modern Cisco switch, such a VoIP/data jack might be configured like:
interface x
switchport
switchport mode access
switchport access vlan 10
switchport voice vlan 100
But if had a old Cisco switch, that didn't "understand" voice VLANs, you might accomplish the same by:
interface x
switchport
switchport trunk encapsulation dot1q
switchport mode trunk
switchport trunk allowed vlan 10,100
switchport trunk native vlan 10
NB: an old Cisco switch that didn't support voice VLANs probably wouldn't support .Q either.
