The customs check is basically first for carry on when you enter the first airport in EU. Then it is for your checked luggage when you pass the customs at you destination.

You have to take the green lane and have no green stripes on your luggage if entering outside of EU. Intra EU you take the blue lane and have green stripes on the luggage tag (obviously no check-in luggage you can as well take the blue lane at destination)

Red lane always if you have something to declare.