I put my tweets in the door, about 4" above the stock grill. I played around with the tweets before I decided where to mount them (door off, just moving tweet around to where it sounded best.) Imaging was better when the tweet was in the sail, but the sound was too off axis for my taste (notes were coming from diff directions.) The location I chose was the best compromise between sound imaging and point-source (any lower on tweet made sound like music was coming to much from your feet.)
The easiest and cleanest way to flush mount in your door is to use a hole saw. Just buy the right bit for your drill and you can make a perfect hole in ~10 secs. The saw is around ~$10. Not really cheap, but if you've spent $1000 on you sys, spend the bit extra to ake sure it goes together right and looks good.