Do you use MC Command Center's story progression or the game's?

The best thing to do is read the documentation on deaderpools website. There is also a thread in the mods section where you can post a question and they will help you with it. To me MCCC is very useful and once you get to looking at all the different tabs it's pretty self explanatory. That's not to say it was super easy for me when I first started using it. I just fooled around with the settings and read up on it.