First of all, you need to get Permission before you start publishing your own PPC stories. The PPC Wiki contains more information on what getting Permission means, exactly - basically, it's about you being able to integrate into the community and showing that you understand the PPC universe and can write good stories in it.

The Permission process also covers the next two steps for writing a PPC story: having at least one agent character you're planning to work with, and choosing a badfic for your first mission. If you've got these, you can dissect the badfic however you like - if you read enough missions, you'll see the basics of the process. Before you publish, you'll need to find at least one beta reader who looks at it and helps you edit and polish it, although I personally recommend having multiple betas for your first mission, if not for later ones. The general policy is that we don't post drafts of missions or unbeta'd stuff on the Board, only finished stories.

This is the gist of it, but if you hang out with us PPCers long enough, you'll see in more detail how it works. It's not at all complicated, just have patience until you get Permission. :)