Hi Pushkar,
Native vlan is a whole whose ethernet frames on sent untagged.Cisco has made the use of Native vllan on its swithces.
http://en.wikipedia.org/wiki/IEEE_802.1Q
If you are setting up a trunk on extreme switches, you have to manually TAG each and every vlan on that port. On cisco switches all vlans get tagged bydefault when you enable trunking but in case of Extreme you have manually tag each vlan.Rest look for some configuration guide on extreme website.
HTH,
-amit singh