Fireplaces, Heating Stoves, Flues and Chimneys - Installing Cast Iron Stove

This question may have already been answered. Sorry if it has, my computer skills fall into the same category as my wood working skills, i.e., weekend woodwacker. I'm trying to make both sets of skills better. The question. I have my new wood box stove on the proper floor pad and I have it 36" from the combustible wall. When I actually get to putting in the blue/black stove pipe and cutting a hole in the celing/roof I'm a bit confused. Isn't the celing, rafters and insulation combustible? I suspect that when I actually go buy the pipe, chimney etc, I will be given the answer, but sometimes I worry about the advice of the youngster at Lowes (although they are knowledgable). Also the roof I will be going through is a new steel roof. Will I have some sort of flange to attach? I'm not in any hurry, since it's February here in Alabama and the current temp is around 80. This installation will be a slow, well thought out and executed summer job. Don't want to mess around with our lives. Appreciate any and all advice, even if you tell me to go find a "professional" to do the installation. Small town and might not find anyone to do it. I do plan on having the local fire dept come out and check over the job before the first fire. Thanks again

Jack West