Do you still need them if the barrel is already on the upper reciever( factory insatled)? and how exactly do use the gauges on a semi auto rifle? I know on a bolt action  the bolt closes or it doesnt, Im confused on how this works on a semi auto rifle sience the bolt always closes.

Headspace SHOULD'VE been checked at the factory.  I don't know anyone who doesn't atleast check the headspace before shipping a completed upper out.

As for how to use them:
[url]http://www.combatsimulations.com/ar15/build.htm[/url]

All you really need is a go gauge and a field gauge to check for safety.  Usually only the factory is concerned about the no-go gauge.  They don't want to ship you a rifle that is borderlining the field gauge and will be unsafe after 1k rounds.

Ugh.. I fuggin hate the terms Go and No-Go.