To me a lot depends on your smoker configuration. If your meat is single level, I wouldn't separate. If you have a vertical smoker and can place meat at various levels, you might want to try it. When we do separate, we tend to place the flats in the middle and protect them with points and/or fat above and below.
It does allow for more targeted temperature control, but if not done correctly might dry the meat out a bit.
Long story short, there is no right way.. Good Q and championships are won both ways.