I cook fat side down. I also cook on grates for half the cook and then in pan for the rest - this allows the meat to sit in some au jus and I use the au jus later.
I cook my briskets around 350-375. I say that only to let you know that the most important temp is internal. If your temps on the cooker spike or fall (though hopefully not below 225) that's no real big deal. I usually cook to around 200* internal - but the feel - as has been mentioned - is the most important indicator. Should feel like butter.