It depends on the type of noise you are trying to get rid of. If you want to soften the noise from the engine, then matting the firewall would be the first thing you do. I would suggest doing the doors and floor next. After that, then you can get really picky: the headliner, trunk, etc.
A car fully matted with two layers is silent with a semi in the next lane (city traffic, that is). And I'm not sure how fast you have to be going to hear road/engine noise with two layers, but I know its fast.
One layer will increase your comfort level, if you consider comfort level being more quiet. I like the sound of my SVT so much I couldn't try to block any of it out. The only mat I would put in would be in the trunk and doors (for sound quality).
You always want your Dynamat to be on metal. Period. Except maybe if a certain spot was rattling. If I were matting doors, I would put some on the panel the speaker is attached to and whatever I would on the inside of the one you see from the outside.
The deck you're referring to I think is the rear area between the top of the seats and the rear window.
I don't know if there is any factory soundproofing in the floor. I think it's just carpet.
Dynamatting to decrease noise in your car is a large task. You have to get to and get everything out of the way of where your Mat is going, then you have to clean the surface thoroughly so the Mat sticks better. Dynamat for a Contour probably costs $500-700 a layer. I know you can get similar stuff much cheaper, but I don't know enough about that stuff to talk about it.
Contours are noisy cars. When I had my GL, it was kind of annoying. But the SVT sounds so much sweeter and now I don't mind.
In summary, it's a task to decrease noise in the car. The less noise, the larger the task. It all depends on what you want. Post here if you have any other questions.