I haven't had my AVIC-D3 installed yet, but opened up the box and looked at the parts. There's a square pad that looks like it goes under the GPS antenna (and I've seen it there in some pictures).

Is that thing necessary? I'd like to put the antenna in a spot in the car that is too small for that big thing to fit.

Its magnetic, it allows you to install the antenna it places where there is no metal. It can be cut to size for the particular application.

If you're talking about the metal piece, it's supposed to improve reception. I would use it if at all possible.