I read a very good nugget in the Aaron Franklin's book where he simplifies this debate of fat side up/down for all kinds of meats. He states that he places the fat side OPPOSITE of the direction the heat is coming from.
So if you have a nice giant smoker that circulates heat well and the hotter temps come from the top down then placing fat down would be the way to go according to his practices.
If your heat comes from the bottom up then the fat would be placed facing up.
All of this is to reduce the amount of rendering.
I believe he is NOT much of a believer in the idea that fat will drain into the meat as much as people think. I'm not sure I agree with that part but when I look at what he cooks it makes sense. He is generally cooking very fatty cuts of meat or cuts of meat with good fat distribution throughout (brisket, beef ribs, pork ribs, sausage, etc.) so the meat likely does not need more fat juice to drain into the meat.
So with a fatty cut like bacon where fat is also well distributed I went ahead and placed the fat side opposite of the heat. With my MES40 the heat goes from bottom up so fat side was placed facing up. I did my first 16 pounds of pork belly bacon last weekend and it turned out phenomenal!
Just some insight on my recent cook that may help:
1. I cooked one 8 pound slab at 165F to an internal temp of 145F. It took roughly 12 hours. I applied smoke for 5 hours.
2. I cooked another 8 pound slab to an IT of 145 by putting the smoker at 165F, walked up to 185F after a few hours, then walked up to 200F for the last bit to hurry and finish it. IT came out fine BUT I think rendering was not as bad because I kept the skin on the bacon for this smoke. I would not have liked to do 200F the whole time because I wouldn't want to over render the fat, but I only have this one experience to go off of so feel free to do as you please and report back :)
3. I could easily taste the wood flavoring when the bacon was eaten at 145F (FDA safe IT for Pork) and when the bacon was softly fried for soft bacon eating (my preference is soft). HOWEVER, when the bacon was fried up crispy the I could not tell the difference in wood flavoring between my two different wood smoked bellies of bacon.
Feel free to test this yourself and report back, I would love more feedback on this point if you are doing two different wood smoked bacons.
Also see the link below to check out my very detailed (and lengthy lol) post on my bacon run this weekend. I did a lot of research before my bacon attempt and still could not find answers to a number of areas I had questions about so I figured I would try and figure them out with my bacon smoke. With all the things I tried, tested, and posted about you might find 1 or 2 things that may be helpful for you. Best of luck!
http://www.smokingmeatforums.com/forum/newestpost/259287