Hi
The native vlan is the vlan in which packets are not tagged. It is there to allow 802.1q interoperability with 802.3 ports.
You should not leave your native vlan as vlan 1. Nor should you use the management vlan. Best practice is to use an unused vlan that has no switchports allocated to it and has no layer 3 SVI associated with it so that it is not routable. We use vlan 999 in our datacentres for the native vlan on trunk links.
You can make any vlan the native vlan but as stated best to use a totally separate vlan for this purpose.
Attached is a link to 6500 vlan security which covers the concept of the native vlan and the problems associated with it.
http://www.cisco.com/en/US/products/hw/switches/ps708/products_white_paper09186a008013159f.shtml#wp39211
HTH
Jon