#1 - for the windows you can make a boolean Select the box ->Boolean->select " Subtract (B-A), then select operand button and click on the fuselage. With any luck, you'll have the " windows" cut out.
#2 - Create a spline, shape it to the window form, and use the shape merge tool. (click on the fuselage, compound objects->shape merge; select shape and click on the spline you just formed.
This will trace the shape onto the fuselage.