If you are going to ceiling mount your projector, then my advise would be to either put your equipment on a shelf in the back of the room, or on a shelf in the closet.
If you put it in the closet, I would remove the bi-fold doors entirely. I would then install trim around the door opening. You could add thin curtains like I talked about above, or if you can keep the closet tidy, then just leave it open.
There are a few reasons I would not put the equipment under the screen. 1) It may limit the size and placement of your screen, 2) It can be more difficult to hide the HDMI cable from your AVR to your projector and 3) You will not have as "clean" a look, and 4) If your equipment has bright lights/displays, it can be distracting.
So I would either put the equipment in the closet (my first choice) or in the back of the room near the ceiling. I would then run the HDMI and power cables for your projector through the ceiling. Here are some pictures of how I did mine (click on the pictures for a larger version, and then click on "Original" if you want the super-size version):
Please note that I usually have my projector mounted more flush with the ceiling, so the cables are much less visible. But when I recently swapped out my old 7500UB for the new 5010, I didn't have any help, and the drop arm extension made it easier for me to do it by myself without dropping the projector. Next time I have a buddy over I'll probably take the extension back out.