Hi, I'm the new editor at BellaOnline for the topic of Feng Shui, and I'm eager to help as much as I can. First of all, is the courtyard door the one that you usually use to enter your home? If you're using Black Hat Sect feng shui, that's the wall (or corner) where the bagua should be placed. Whether or not the door is recessed doesn't affect the bagua. Even if your door is deeply recessed inside the house to that middle row of colors, the bottom (Knowledge, Career, and Helpful People) goes along the wall you "pass through" to enter the home.
Does this help? If not, or if you need more advice, please ask. Thanks for reading!