In terms of getting useful heat from the controller, I think it is almost a moot point.
One COULD put the controller inside the passenger compartment of the car the gain the little bit of heat, but then it's adding heat in the summer too!
My experience with controllers is that there is so little heat coming off of it, it's not worth messing around with.
My charger, on the other hand, does put out a bit of heat. That is installed inside the passenger compartment. In the grand scheme though, it's not putting out that much heat.
Paul, I know it's getting ahead, but have you thought about an enclosure yet? The latest e-mail from INSTRUCTABLES had a nice little bit about making boxes out of acrylic with T-bolts.
How to Make Anything (Using Acrylic and Machine Screws)
I have seen some other controllers with acrylic boxes that looked really nice.
Plus, your controller just looks so dang cool, it would be a shame to put it in a plain black metal box.