is it better used in the stock air box or used out the air box like a regular intake...?

 

Are you talking about the box that the factory filter is enclosed in?

If yes, then keeping it enclosed will probably get you colder air, if you leave the cover off then you are sucking in engine compartment air which is similar to that of a non-cai intake. Warm air.

 

I use it covered it makes a difference. If you have the filter exposed you will suck in hot air. With it covered you have a cai. That is how mine is set up. Just remove the resonator.