I am working on my first scene so i am using the template and in the template the scenes default name is Mission Template but if i change it to anything other than that, the mission no longer apears in campaign?

That's because everything else in the scene is still checking for a "Mission Template" to apply everything to. Renaming a file unfortunately won't change all of the references to that name. You have to go through the ini and replace each instance of "Mission Template" with your preferred name.

Also, this should be in Support.

But the file name of the mission is not what is messing up. I have that part working ok. I tried to change what the name of the mission is in campaign by changing the PresentName in AddScene = Scene to the name i wanted. Instead should i change SceneName in AddActivity = GAScripted?

No. Just replace what ever it was to what ever the scene is called.

Say we started new, everything is called 'Mission Template' you want to replace every instance of 'Mission Template' with your new scene name, say 'Last Chance' (A scene I'm working on).

EDIT: Oh, and also make sure the 'LocationOnPlanet = Vector' isn't set to X = 0
Y = 0
If so, change them. X should be positive, Y should be negative.

Best way to fix this is to upload it here for people to bugfix.