Paint.NET :: Do Colours Show Through When Using Layers

I am in the middle of a huge project and all of a sudden have a major concern.

When I am using layers and the background is a photo of the colour blue (rectangular shape).Now as a new layer, I am pasting another photo (a smaller rectangular shape) on top,with say a car in the middle.

Then saving this 'montage' as one jpeg.Now, when printing this image, would the blue colour that is physically under the smaller car photo shine through underneath? Or would it only print and use what is physically shown, despite me knowing that underneath there is another darker colour?

(As the end result should just show the smaller rectangular photo with the car and that one being surrounded by a blue border.)