You may or may not like the sound of just dropping into the stock locations but loading into the glass is definitely going to cause some issues with the sound waves coming out of those drivers. Might work out in your favor but might not. At the end of the day none of us are the ones who have to listen to it, so give it a whirl and if it doesn't sound good at least you'll have tunes while you're driving around thinking about how much effort you're willing to go through in creating better mounting locations.
