I like cooking chili for hours; 3 minimum, 4 is perfect. Since brisket flat and chuck roasts are both cut from the same part of the animal, the real question is how much fat do you want in your chili? The chuck roast will be fattier.
Personally, when I do chili with fresh smoked beef, I only leave it in the smoker until it stalls. By then, there's enough smoke on the beef to carry into the chili. Then I take it out of the smoker, cube it up, and build my chili in a Dutch Oven on the stovetop. I bring it to a simmer then let it go.