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Check to see if the tuner you are running has any particular setting that maybe you can change. The H&S has a setting just for that, I guess some people want to produce thick black clouds of smoke just because, I guess to some degree it might help on the performance end but that's not for me.
the h&s setting is called LBF Low Boost Fuel i think it is a 1-5 setting i had mine on 3 (more fuel) and lowered it to 1 (Less Fuel) to try for better fuel economy, yes it smokes more but i did notice a difference in power off the line.
the main thing for your problem of having too much black smoke would be that it is not getting enoughh air, boost. so to make sure you have good air you need to make sure your air filter is not fully plugged of crap, make sure no intercooler boots came off which would cause the truck to not boost very well or at all. if the boost gauge does not move much ever possibly turbo problems.