Laptop in a suitcase

When I go to airport, I recall following this procedure:

Go at the kiosks (? how do we call them?) and the service person from the airliner will make sure my ticket is OK and will ask for my suitcase, which I give it right there.

Then, when I am checked later on (you know where they ask you to take off your watch, belt, etc.), they will ask about laptops, and if I have one, they will open the tray and make sure it's a laptop.

However, what about the case that the laptop is in the suitcase?

I do not want them to freak out when they see it in there (don't worry about its safety). It will be accompanied by 2 chargers and 2 mouses.

_{If it matters, I will be traveling from San Francisco, to a destination in Europe, via transit in another European city.}