whenver i vist there bases i can kill everybody but the main chief/person he just kneels to the ground for a bit then gets back up. ive completed the main quest and sided with the others, any ideas?

It's the same with the Imperial Legion camps. An oversight (read: unmitigated balls-up) by Bethesda. There's nothing you can do, unless you're on PC.

seriously wtf how could they just overlook sumit like that

By being numpties

There is a mod in the workshop called I think Kill those general that lets you kill the camp leaders.

When I use Setessential it asks for what NPC.

Do I have to find the code for every legate/Stormcloak officer at each camp, or am I doing it wrong.

Yes, you need their base ID. It should be available on UESP.